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Improved parsing of GN in the SwissProt parser, take 2 (#4162)

Browse Source 
* updated SwissProt files

* all tests passing

* update
This commit is contained in:
mdehoon
2022-11-16 00:09:53 +09:00
committed by GitHub
parent 1cc8eb1573
commit 3e631655d7
27 changed files with 10875 additions and 2788 deletions
Download Patch File Download Diff File Expand all files Collapse all files

50
Bio/SwissProt/__init__.py
View File

@ -45,7 +45,8 @@ class Record:
- sequence_update A tuple of (date, release).
- annotation_update A tuple of (date, release).
- description Free-format description.
- gene_name Gene name. See userman.txt for description.
- gene_name A list of dictionaries with keys 'Name', 'Synonyms',
'OrderedLocusNames' and 'ORFNames'.
- organism The source of the sequence.
- organelle The origin of the sequence.
- organism_classification The taxonomy classification. List of strings.
@ -67,21 +68,21 @@ class Record:
Examples
--------
>>> from Bio import SwissProt
>>> example_filename = "SwissProt/sp008"
>>> example_filename = "SwissProt/P68308.txt"
>>> with open(example_filename) as handle:
... records = SwissProt.parse(handle)
... for record in records:
... print(record.entry_name)
... print(",".join(record.accessions))
... print(record.accessions)
... print(record.keywords)
... print(repr(record.organism))
... print(record.organism)
... print(record.sequence[:20] + "...")
...
1A02_HUMAN
P01892,P06338,P30514,P30444,P30445,P30446,Q29680,Q29899,Q95352,Q29837,Q95380
['MHC I', 'Transmembrane', 'Glycoprotein', 'Signal', 'Polymorphism', '3D-structure']
'Homo sapiens (Human).'
MAVMAPRTLVLLLSGALALT...
NU3M_BALPH
['P68308', 'P24973']
['Electron transport', 'Membrane', 'Mitochondrion', 'Mitochondrion inner membrane', 'NAD', 'Respiratory chain', 'Translocase', 'Transmembrane', 'Transmembrane helix', 'Transport', 'Ubiquinone']
Balaenoptera physalus (Fin whale) (Balaena physalus).
MNLLLTLLTNTTLALLLVFI...
"""
@ -98,7 +99,7 @@ class Record:
self.annotation_update = None
self.description = []
self.gene_name = ""
self.gene_name = []
self.organism = []
self.organelle = ""
self.organism_classification = []
@ -304,9 +305,7 @@ def _read(handle):
elif key == "DE":
record.description.append(value.strip())
elif key == "GN":
if record.gene_name:
record.gene_name += " "
record.gene_name += value
_read_gn(record, value)
elif key == "OS":
record.organism.append(value)
elif key == "OG":
@ -406,6 +405,31 @@ def _read(handle):
raise ValueError("Unexpected end of stream.")
def _read_gn(record, value):
tokens = value.rstrip(";").split("; ")
try:
gene_name = record.gene_name[-1]
except IndexError:
pass
for token in tokens:
if token.startswith("Name="):
name = token[5:]
gene_name = {"Name": name}
record.gene_name.append(gene_name)
else:
for keyword in ("Synonyms", "OrderedLocusNames", "ORFNames"):
if token.startswith(keyword + "="):
token = token[len(keyword) + 1 :]
gene_name[keyword] = token.rstrip(",").split(", ")
break
else:
keyword = list(record.gene_name[-1].keys())[-1]
if keyword == "Name":
gene_name[keyword] += " " + token
else:
gene_name[keyword] += token.rstrip(",").split(", ")
def _read_id(record, line):
cols = line[5:].split()
# Prior to release 51, included with MoleculeType:

3
NEWS.rst
View File

@ -65,6 +65,9 @@ to the test suite.
Add new ``gc_fraction`` function in ``SeqUtils`` and marks ``GC`` for future
deprecation.
Support for the old format (dating back to 2004) of the GN line in SwissProt
files was dropped in ``Bio.SwissProt``.
Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

533
Tests/Registry/EDD_RAT.dat
View File

@ -1,96 +1,471 @@
ID EDD_RAT STANDARD; PRT; 920 AA.
AC Q62671;
DT 01-NOV-1997 (Rel. 35, Created)
DT 15-JUN-2002 (Rel. 41, Last sequence update)
DT 15-JUN-2002 (Rel. 41, Last annotation update)
DE Ubiquitin--protein ligase EDD (EC 6.3.2.-) (Hyperplastic discs
DE protein homolog) (100 kDa protein) (Fragment).
GN EDD OR HYD.
ID UBR5_RAT Reviewed; 2788 AA.
AC Q62671; F1LRS0;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 22-FEB-2012, sequence version 3.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=E3 ubiquitin-protein ligase UBR5;
DE EC=2.3.2.26;
DE AltName: Full=100 kDa protein;
DE AltName: Full=E3 ubiquitin-protein ligase, HECT domain-containing 1;
DE AltName: Full=HECT-type E3 ubiquitin transferase UBR5;
DE AltName: Full=Hyperplastic discs protein homolog;
GN Name=Ubr5; Synonyms=Dd5, Edd, Edd1, Hyd;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus.
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP SEQUENCE FROM N.A.
RC STRAIN=Wistar; TISSUE=Testis;
RA Mueller D., Rehbein M., Baumeister H., Richter D.;
RT "Molecular characterization of a novel rat protein structurally
RT related to poly(A) binding proteins and the 70K protein of the U1
RT small nuclear ribonucleoprotein particle (snRNP).";
RL Nucleic Acids Res. 20:1471-1475(1992).
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [2]
RP ERRATUM.
RP NUCLEOTIDE SEQUENCE [MRNA] OF 1868-2788.
RC STRAIN=Wistar; TISSUE=Testis;
RX PubMed=1533713; DOI=10.1093/nar/20.7.1471;
RA Mueller D., Rehbein M., Baumeister H., Richter D.;
RT "Molecular characterization of a novel rat protein structurally related to
RT poly(A) binding proteins and the 70K protein of the U1 small nuclear
RT ribonucleoprotein particle (snRNP).";
RL Nucleic Acids Res. 20:1471-1475(1992).
RN [3]
RP ERRATUM OF PUBMED:1533713.
RA Mueller D., Rehbein M., Baumeister H., Richter D.;
RL Nucleic Acids Res. 20:2624-2624(1992).
RN [3]
RN [4]
RP IDENTIFICATION OF PROBABLE FRAMESHIFT.
RX PubMed=10030672; DOI=10.1038/sj.onc.1202249;
RA Callaghan M.J., Russell A.J., Woollatt E., Sutherland G.R.,
RA Sutherland R.L., Watts C.K.W.;
RT "Identification of a human HECT family protein with homology to the
RT Drosophila tumor suppressor gene hyperplastic discs.";
RL Oncogene 17:3479-3491(1998).
CC -!- FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from
CC an E2 ubiquitin-conjugating enzyme in the form of a thioester and
CC then directly transfers the ubiquitin to targeted substrates (By
CC similarity). May be involved in maturation and/or post-
CC transcriptional regulation of mRNA. May play a role in control of
CC cell cycle progression. May have tumor suppressor function.
CC Regulates DNA topoisomerase II binding protein (TopBP1) for the
CC DNA damage response (By similarity).
CC -!- SUBCELLULAR LOCATION: Nuclear (By similarity).
CC -!- TISSUE SPECIFICITY: Highest levels found in testis. Also present
CC in liver, kidney, lung and brain.
CC -!- DEVELOPMENTAL STAGE: In early post-natal life, expression in
CC the testis increases to reach a maximum around day 28.
CC -!- MISCELLANEOUS: A cysteine residue is required for ubiquitin-
CC thiolester formation.
CC -!- SIMILARITY: CONTAINS 1 HECT-TYPE E3 UBIQUITIN-PROTEIN LIGASE
CC DOMAIN.
CC -!- CAUTION: Ref.1 sequence differs from that shown due to a
CC frameshift in position 30.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; X64411; CAA45756.1; ALT_FRAME.
DR HSSP; O95071; 1I2T.
DR InterPro; IPR000569; HECT_domain.
DR InterPro; IPR002004; PABP/HECT.
RN [5]
RP TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX PubMed=12239083; DOI=10.1210/en.2002-220262;
RA Oughtred R., Bedard N., Adegoke O.A.J., Morales C.R., Trasler J.,
RA Rajapurohitam V., Wing S.S.;
RT "Characterization of rat100, a 300-kilodalton ubiquitin-protein ligase
RT induced in germ cells of the rat testis and similar to the Drosophila
RT hyperplastic discs gene.";
RL Endocrinology 143:3740-3747(2002).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-2231 AND SER-2475, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
CC -!- FUNCTION: E3 ubiquitin-protein ligase which is a component of the N-end
CC rule pathway. Recognizes and binds to proteins bearing specific N-
CC terminal residues that are destabilizing according to the N-end rule,
CC leading to their ubiquitination and subsequent degradation (By
CC similarity). Involved in maturation and/or transcriptional regulation
CC of mRNA by activating CDK9 by polyubiquitination. May play a role in
CC control of cell cycle progression. May have tumor suppressor function.
CC Regulates DNA topoisomerase II binding protein (TopBP1) for the DNA
CC damage response. Plays an essential role in extraembryonic development.
CC Ubiquitinates acetylated PCK1. Also acts as a regulator of DNA damage
CC response by acting as a suppressor of RNF168, an E3 ubiquitin-protein
CC ligase that promotes accumulation of 'Lys-63'-linked histone H2A and
CC H2AX at DNA damage sites, thereby acting as a guard against excessive
CC spreading of ubiquitinated chromatin at damaged chromosomes (By
CC similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC EC=2.3.2.26;
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC -!- SUBUNIT: Binds TOPBP1. Associates with CDK9 and TFIIS/TCEA1 and forms a
CC transcription regulatory complex made of CDK9, RNAP II, UBR5 and
CC TFIIS/TCEA1 that can stimulate target gene transcription by recruiting
CC their promoters. Interacts with PIH1D1. {ECO:0000250|UniProtKB:O95071}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Highest levels found in testis. Also present in
CC liver, kidney, lung and brain. {ECO:0000269|PubMed:12239083}.
CC -!- DEVELOPMENTAL STAGE: In early postnatal life, expression in the testis
CC increases to reach a maximum around day 28.
CC {ECO:0000269|PubMed:12239083}.
CC -!- MISCELLANEOUS: A cysteine residue is required for ubiquitin-thioester
CC formation.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA45756.1; Type=Frameshift; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; X64411; CAA45756.1; ALT_FRAME; mRNA.
DR PIR; S22659; S22659.
DR PDB; 3NTW; X-ray; 2.60 A; A/C=2383-2442.
DR PDBsum; 3NTW; -.
DR SMR; Q62671; -.
DR ELM; Q62671; -.
DR IntAct; Q62671; 1.
DR STRING; 10116.ENSRNOP00000009115; -.
DR iPTMnet; Q62671; -.
DR PhosphoSitePlus; Q62671; -.
DR jPOST; Q62671; -.
DR PaxDb; Q62671; -.
DR UCSC; RGD:621236; rat.
DR RGD; 621236; Ubr5.
DR eggNOG; KOG0943; Eukaryota.
DR InParanoid; Q62671; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q62671; -.
DR Proteomes; UP000002494; Unplaced.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:RGD.
DR GO; GO:0005634; C:nucleus; ISO:RGD.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; ISO:RGD.
DR GO; GO:0032991; C:protein-containing complex; ISO:RGD.
DR GO; GO:0019904; F:protein domain specific binding; IDA:RGD.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0043130; F:ubiquitin binding; IEA:InterPro.
DR GO; GO:0061630; F:ubiquitin protein ligase activity; IDA:RGD.
DR GO; GO:0034450; F:ubiquitin-ubiquitin ligase activity; ISO:RGD.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; ISS:UniProtKB.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR GO; GO:2000780; P:negative regulation of double-strand break repair; ISS:UniProtKB.
DR GO; GO:1901315; P:negative regulation of histone H2A K63-linked ubiquitination; ISS:UniProtKB.
DR GO; GO:0032700; P:negative regulation of interleukin-17 production; ISO:RGD.
DR GO; GO:0090263; P:positive regulation of canonical Wnt signaling pathway; ISO:RGD.
DR GO; GO:0010628; P:positive regulation of gene expression; ISO:RGD.
DR GO; GO:0042307; P:positive regulation of protein import into nucleus; ISO:RGD.
DR GO; GO:0050847; P:progesterone receptor signaling pathway; ISO:RGD.
DR GO; GO:0070936; P:protein K48-linked ubiquitination; ISO:RGD.
DR GO; GO:0000209; P:protein polyubiquitination; ISO:RGD.
DR GO; GO:0016567; P:protein ubiquitination; IDA:RGD.
DR GO; GO:2000779; P:regulation of double-strand break repair; IBA:GO_Central.
DR GO; GO:0031647; P:regulation of protein stability; ISO:RGD.
DR CDD; cd14423; CUE_UBR5; 1.
DR Gene3D; 2.130.10.30; -; 1.
DR InterPro; IPR024725; E3_UbLigase_EDD_UBA.
DR InterPro; IPR000569; HECT_dom.
DR InterPro; IPR035983; Hect_E3_ubiquitin_ligase.
DR InterPro; IPR036053; PABP-dom.
DR InterPro; IPR002004; PABP_HYD.
DR InterPro; IPR009091; RCC1/BLIP-II.
DR InterPro; IPR003126; Znf_UBR.
DR Pfam; PF11547; E3_UbLigase_EDD; 1.
DR Pfam; PF00632; HECT; 1.
DR Pfam; PF00658; PABP; 1.
DR SMART; SM00119; HECTc; 1.
DR SMART; SM00517; PolyA; 1.
DR SMART; SM00396; ZnF_UBR1; 1.
DR SUPFAM; SSF50985; SSF50985; 1.
DR SUPFAM; SSF56204; SSF56204; 1.
DR SUPFAM; SSF63570; SSF63570; 1.
DR PROSITE; PS50237; HECT; 1.
KW Ubl conjugation pathway; Ligase; Nuclear protein.
FT NON_TER 1 1
FT DOMAIN 515 571 PABP-LIKE.
FT DOMAIN 583 920 HECT.
FT DOMAIN 108 119 ASP/GLU-RICH (ACIDIC).
FT DOMAIN 158 181 PRO-RICH.
FT DOMAIN 451 470 ARG/GLU-RICH (MIXED CHARGE).
FT DOMAIN 479 488 ARG/ASP-RICH (MIXED CHARGE).
FT DOMAIN 610 621 ASP/GLU-RICH (ACIDIC).
FT DOMAIN 858 878 PRO-RICH.
FT BINDING 889 889 UBIQUITIN (BY SIMILARITY).
SQ SEQUENCE 920 AA; 103949 MW; 465771084536C3AA CRC32;
ARRERMTARE EASLRTLEGR RRATLLSARQ GMMSARGDFL NYALSLMRSH NDEHSDVLPV
LDVCSLKHVA YVFQALIYWI KAMNQQTTLD TPQLERKRTR ELLELGIDNE DSEHENDDDT
SQSATLNDKD DESLPAETGQ NHPFFRRSDS MTFLGCIPPN PFEVPLAEAI PLADQPHLLQ
PNARKEDLFG RPSQGLYSSS AGSGKCLVEV TMDRNCLEVL PTKMSYAANL KNVMNMQNRQ
KKAGEDQSML AEEADSSKPG PSAHDVAAQL KSSLLAEIGL TESEGPPLTS FRPQCSFMGM
VISHDMLLGR WRLSLELFGR VFMEDVGAEP GSILTELGGF EVKESKFRRE MEKLRNQQSR
DLSLEVDRDR DLLIQQTMRQ LNNHFGRRCA TTPMAVHRVK VTFKDEPGEG SGVARSFYTA
IAQAFLSNEK LPNLDCIQNA NKGTHTSLMQ RLRNRGERDR EREREREMRR SSGLRAGSRR
DRDRDFRRQL SIDTRPFRPA SEGNPSDDPD PLPAHRQALG ERLYPRVQAM QPAFASKITG
MLLELSPAQL LLLLASEDSL RARVEEAMEL IVAHGRENGA DSILDLGLLD SSEKVQENRK
RHGSSRSVVD MDLDDTDDGD DNAPLFYQPG KRGFYTPRPG KNTEARLNCF RNIGRILGLC
LLQNELCPIT LNRHVIKVLL GRKVNWHDFA FFDPVMYESL RQLILASQSS DADAVFSAMD
LAFAVDLCKE EGGGQVELIP NGVNIPVTPQ NVYEYVRKYA EHRMLVVAEQ PLHAMRKGLL
DVLPKNSLED LTAEDFRLLV NGCGEVNVQM LISFTSFNDE SGENAEKLLQ FKRWFWSIVE
RMSMTERQDL VYFWTSSPSL PASEEGFQPM PSITIRPPDD QHLPTANTCI SRLYVPLYSS
KQILKQKLLL AIKTKNFGFV
DR PROSITE; PS51309; PABC; 1.
DR PROSITE; PS51157; ZF_UBR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; Metal-binding; Nucleus;
KW Phosphoprotein; Reference proteome; Transferase; Ubl conjugation pathway;
KW Zinc; Zinc-finger.
FT CHAIN 1..2788
FT /note="E3 ubiquitin-protein ligase UBR5"
FT /id="PRO_0000086933"
FT DOMAIN 2367..2444
FT /note="PABC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00641"
FT DOMAIN 2451..2788
FT /note="HECT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00104"
FT ZN_FING 1166..1234
FT /note="UBR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00508"
FT REGION 68..165
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 318..343
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 572..636
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 988..1024
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1041..1064
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1288..1308
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1504..1729
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1848..1881
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1974..2011
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 2106..2132
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 2313..2383
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 2463..2490
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 77..141
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 318..334
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 572..591
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 600..621
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1006..1020
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1041..1061
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1510..1540
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1552..1566
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1567..1597
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1611..1640
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1649..1674
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1682..1729
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1865..1881
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1986..2004
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 2319..2360
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 2463..2480
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 2757
FT /note="Glycyl thioester intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00104"
FT MOD_RES 100
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 317
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 342
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 567
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 601
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 626
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 797
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 917
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1007
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1104
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1124
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1216
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1297
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1344
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1364
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1470
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1538
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1725
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1730
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1735
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1769
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1959
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 1980
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 2016
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 2018
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 2020
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 2066
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 2203
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 2231
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 2279
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 2459
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 2473
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95071"
FT MOD_RES 2475
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT CONFLICT 1890
FT /note="Missing (in Ref. 2; CAA45756)"
FT /evidence="ECO:0000305"
FT HELIX 2383..2396
FT /evidence="ECO:0007829|PDB:3NTW"
FT HELIX 2400..2402
FT /evidence="ECO:0007829|PDB:3NTW"
FT HELIX 2403..2410
FT /evidence="ECO:0007829|PDB:3NTW"
FT HELIX 2415..2423
FT /evidence="ECO:0007829|PDB:3NTW"
FT HELIX 2425..2439
FT /evidence="ECO:0007829|PDB:3NTW"
SQ SEQUENCE 2788 AA; 308027 MW; C2EA68B962627231 CRC64;
MNKQAVKRLH MLREVSEKLN KYNLNSHPPL NVLEQATIKQ CVVGPNHAAF LLEDGRICRI
GFSVQPDRLE LGKPDNNDGS KLNSSSGTGR TSRPGRTSDS PWFLSGSETL GRLAGNTLGS
RWSSGVGGSG GGSSGRSSAG ARDSRRQTRV IRTGRDRGSG LLGSQPQPVI PASVIPEELI
SQAQVVLQGK SRSVIIRELQ RTNLDVNLAV NNLLSRDDED GDDGDDTASE SYLPGEDLMS
LLDADIHSAH PSVIIDADAM FSEDISYFGY PSFRRSSLSR LGSSRVLLLP LERDSELLRE
RESVLRLRER RWLDGASFDN ERGSTSKEGE PNPDKKNTPV QSPVSLGEDL QWWPDKDGTK
FTCIGALYSE LVAVSSKGEL YQWKWTESEP YRNAQNPSLH HPRATFLGLT NEKIVLLSAN
SIRATVATEN NKVATWVDET LSSVASKLEH TAQTYSELQG ERIVSLHCCA LYTCAQLENN
LYWWGVVPFS QRKKMLEKAR AKNKKPKSSA GVQSLNVRGG RQVCLRNNPL YHAGAVAFSI
SAGIPKVGVL MESVWNMNDS CRFQLRSPES LKSMEKASKT IETKPESKQE PVKTEMGPPP
SPASTCSDAS SIASSASMPY KRRRSTPAPK EEEKVNEEQW SLREVVFVED VKNVPVGKVL
KVDGAYVAVK FPGTSSNTNC QNSSGPDADP SSLLQDCRLL RIDELQVVKT GGTPKVPDCF
QRTPKKLCIP EKTEILAVNV DSKGVHAVLK TGNWVRYCIF DLATGKAEQE NNFPTSSVAF
LGQNERSVAI FTAGQESPII LRDGNGTIYP MAKDCMGGIR DPDWLDLPPI SSLGMGVHSL
INLPANSTIK KKAAIIIMAV EKQTLMQHIL RCDYEACRQY LVNLEQAVVL EQNLQMLQTF
ISHRCDGNRN ILHACVSVCF PTSNKETKEE EEAERSERNT FAERLSAVEA IANAISVVSS
NGPGNRAGSS SSRSLRLREM MRRSLRAAGL GRHEAGASSS DHQDPVSPPI APPSWVPDPP
SMDPDGDIDF ILAPAVGSLT TAATGGGQGP STSTIPGPST EPSVVESKDR KANAHFILKL
LCDSAVLQPY LRELLSAKDA RGMTPFMSAV SGRAYPAAIT ILETAQKIAK AEVSGSEKEE
DVFMGMVCPS GTNPDDSPLY VLCCNDTCSF TWTGAEHINQ DIFECRTCGL LESLCCCTEC
ARVCHKGHDC KLKRTSPTAY CDCWEKCKCK TLIAGQKSAR LDLLYRLLTA TNLVTLPNSR
GEHLLLFLVQ TVARQTVEHC QYRPPRIRED RNRKTASPDD SDMPDHDLEP PRFAQLALER
VLQDWNALRS MIMFGSQENK DPLSASSRIG HLLPEEQVYL NQQSGTIRLD CFTHCLIVKC
TADILLLDTL LGTLVKELQN KYTPGRREEA IAVTMRFLRS VARVFVILSV EMASSKKKNN
FIPQPIGKCK RVFQALLPYA VEELCNVAES LIVPVRMGIA RPTAPFTLAS TSIDAMQGSE
ELFSVEPLPP RPSSDQSSSS SQSQSSYIIR NPQQRRISQS QPVRGREEEQ DDIVSADVEE
VEVVEGVAGE EDHHDEQEEH GEENAEAEGH HDEHDEDGSD MELDLLAAAE TESDSESNHS
NQDNASGRRS VVTAATAGSE AGASSVPAFF SEDDSQSNDS SDSDSSSSQS DDIEQETFML
DEPLERTTNS SHANGAAQAP RSMQWAVRNT QHQRAASTAP SSTSTPAASS AGLIYIDPSN
LRRSGTISTS AAAAAAALEA SNASSYLTSA SSLARAYSIV IRQISDLMGL IPKYNHLVYS
QIPAAVKLTY QDAVNLQNYV EEKLIPTWNW MVSIMDSTEA QLRYGSALAS AGDPGHPNHP
LHASQNSARR ERMTAREEAS LRTLEGRRRR ATLLSARQGM MSARGDFLNY ALSLMRSHND
EHSDVLPVLD VCSLKHVAYV FQALIYWIKA MNQQTTLDTP QLERKRTREL LELGIDNEDS
EHENDDDTSQ SATLNDKDDE SLPAETGQNH PFFRRSDSMT FLGCIPPNPF EVPLAEAIPL
ADQPHLLQPN ARKEDLFGRP SQGLYSSSAG SGKCLVEVTM DRNCLEVLPT KMSYAANLKN
VMNMQNRQKK AGEDQSMLAE EADSSKPGPS AHDVAAQLKS SLLAEIGLTE SEGPPLTSFR
PQCSFMGMVI SHDMLLGRWR LSLELFGRVF MEDVGAEPGS ILTELGGFEV KESKFRREME
KLRNQQSRDL SLEVDRDRDL LIQQTMRQLN NHFGRRCATT PMAVHRVKVT FKDEPGEGSG
VARSFYTAIA QAFLSNEKLP NLDCIQNANK GTHTSLMQRL RNRGERDRER EREREMRRSS
GLRAGSRRDR DRDFRRQLSI DTRPFRPASE GNPSDDPDPL PAHRQALGER LYPRVQAMQP
AFASKITGML LELSPAQLLL LLASEDSLRA RVEEAMELIV AHGRENGADS ILDLGLLDSS
EKVQENRKRH GSSRSVVDMD LDDTDDGDDN APLFYQPGKR GFYTPRPGKN TEARLNCFRN
IGRILGLCLL QNELCPITLN RHVIKVLLGR KVNWHDFAFF DPVMYESLRQ LILASQSSDA
DAVFSAMDLA FAVDLCKEEG GGQVELIPNG VNIPVTPQNV YEYVRKYAEH RMLVVAEQPL
HAMRKGLLDV LPKNSLEDLT AEDFRLLVNG CGEVNVQMLI SFTSFNDESG ENAEKLLQFK
RWFWSIVERM SMTERQDLVY FWTSSPSLPA SEEGFQPMPS ITIRPPDDQH LPTANTCISR
LYVPLYSSKQ ILKQKLLLAI KTKNFGFV
//

403
Tests/SwissProt/O95832.txt Normal file
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@ -0,0 +1,403 @@
ID CLD1_HUMAN Reviewed; 211 AA.
AC O95832;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 12-OCT-2022, entry version 186.
DE RecName: Full=Claudin-1;
DE AltName: Full=Senescence-associated epithelial membrane protein;
GN Name=CLDN1; Synonyms=CLD1, SEMP1; ORFNames=UNQ481/PRO944;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND TISSUE SPECIFICITY.
RX PubMed=9931503; DOI=10.1016/s0378-1119(98)00553-8;
RA Swisshelm K.L., Machl A., Planitzer S., Robertson R., Kubbies M.,
RA Hosier S.;
RT "SEMP1, a senescence-associated cDNA isolated from human mammary epithelial
RT cells, is a member of an epithelial membrane protein superfamily.";
RL Gene 226:285-295(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Mitic L.M., Anderson J.M.;
RT "Human claudin-1 isolated from Caco-2 mRNA.";
RL Submitted (DEC-1998) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=10828592; DOI=10.1159/000015553;
RA Halford S., Spencer P., Greenwood J., Winton H., Hunt D.M., Adamson P.;
RT "Assignment of claudin-1 (CLDN1) to human chromosome 3q28-->q29 with
RT somatic cell hybrids.";
RL Cytogenet. Cell Genet. 88:217-217(2000).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=11071387; DOI=10.1007/s004390000375;
RA Kraemer F., White K., Kubbies M., Swisshelm K.L., Weber B.H.F.;
RT "Genomic organization of claudin-1 and its assessment in hereditary and
RT sporadic breast cancer.";
RL Hum. Genet. 107:249-256(2000).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=12975309; DOI=10.1101/gr.1293003;
RA Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J.,
RA Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P.,
RA Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E., Heldens S., Huang A.,
RA Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D.,
RA Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L.,
RA Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C.,
RA Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J.,
RA Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M.;
RT "The secreted protein discovery initiative (SPDI), a large-scale effort to
RT identify novel human secreted and transmembrane proteins: a bioinformatics
RT assessment.";
RL Genome Res. 13:2265-2270(2003).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.;
RT "Cloning of human full open reading frames in Gateway(TM) system entry
RT vector (pDONR201).";
RL Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Urinary bladder;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [8]
RP INVOLVEMENT IN NISCH.
RX PubMed=15521008; DOI=10.1053/j.gastro.2004.07.022;
RA Hadj-Rabia S., Baala L., Vabres P., Hamel-Teillac D., Jacquemin E.,
RA Fabre M., Lyonnet S., De Prost Y., Munnich A., Hadchouel M., Smahi A.;
RT "Claudin-1 gene mutations in neonatal sclerosing cholangitis associated
RT with ichthyosis: a tight junction disease.";
RL Gastroenterology 127:1386-1390(2004).
RN [9]
RP INVOLVEMENT IN NISCH.
RX PubMed=16619213; DOI=10.1002/humu.20333;
RA Feldmeyer L., Huber M., Fellmann F., Beckmann J.S., Frenk E., Hohl D.;
RT "Confirmation of the origin of NISCH syndrome.";
RL Hum. Mutat. 27:408-410(2006).
RN [10]
RP FUNCTION (MICROBIAL INFECTION), AND MUTAGENESIS OF ILE-32 AND GLU-48.
RX PubMed=17325668; DOI=10.1038/nature05654;
RA Evans M.J., von Hahn T., Tscherne D.M., Syder A.J., Panis M., Wolk B.,
RA Hatziioannou T., McKeating J.A., Bieniasz P.D., Rice C.M.;
RT "Claudin-1 is a hepatitis C virus co-receptor required for a late step in
RT entry.";
RL Nature 446:801-805(2007).
RN [11]
RP FUNCTION (MICROBIAL INFECTION), SUBCELLULAR LOCATION, INTERACTION WITH
RP OCLN; CD81; CLDN4; CLDN6 AND CLDN9, AND MUTAGENESIS OF ILE-32 AND GLU-48.
RX PubMed=20375010; DOI=10.1074/jbc.m110.104836;
RA Harris H.J., Davis C., Mullins J.G., Hu K., Goodall M., Farquhar M.J.,
RA Mee C.J., McCaffrey K., Young S., Drummer H., Balfe P., McKeating J.A.;
RT "Claudin association with CD81 defines hepatitis C virus entry.";
RL J. Biol. Chem. 285:21092-21102(2010).
RN [12]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [13]
RP INTERACTION WITH CD81.
RX PubMed=21516087; DOI=10.1038/nm.2341;
RA Lupberger J., Zeisel M.B., Xiao F., Thumann C., Fofana I., Zona L.,
RA Davis C., Mee C.J., Turek M., Gorke S., Royer C., Fischer B., Zahid M.N.,
RA Lavillette D., Fresquet J., Cosset F.L., Rothenberg S.M., Pietschmann T.,
RA Patel A.H., Pessaux P., Doffoel M., Raffelsberger W., Poch O.,
RA McKeating J.A., Brino L., Baumert T.F.;
RT "EGFR and EphA2 are host factors for hepatitis C virus entry and possible
RT targets for antiviral therapy.";
RL Nat. Med. 17:589-595(2011).
RN [14]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=23407391; DOI=10.1038/jid.2012.507;
RA Kirschner N., Rosenthal R., Furuse M., Moll I., Fromm M., Brandner J.M.;
RT "Contribution of tight junction proteins to ion, macromolecule, and water
RT barrier in keratinocytes.";
RL J. Invest. Dermatol. 133:1161-1169(2013).
RN [15]
RP FUNCTION (MICROBIAL INFECTION), AND INTERACTION WITH DENGUE VIRUS SMALL
RP ENVELOPE PROTEIN M.
RX PubMed=24074594; DOI=10.1016/j.virol.2013.08.009;
RA Che P., Tang H., Li Q.;
RT "The interaction between claudin-1 and dengue viral prM/M protein for its
RT entry.";
RL Virology 446:303-313(2013).
RN [16]
RP SUBCELLULAR LOCATION, AND SUBUNIT.
RX PubMed=23704991; DOI=10.1371/journal.pone.0064517;
RA Bonander N., Jamshad M., Oberthuer D., Clare M., Barwell J., Hu K.,
RA Farquhar M.J., Stamataki Z., Harris H.J., Dierks K., Dafforn T.R.,
RA Betzel C., McKeating J.A., Bill R.M.;
RT "Production, purification and characterization of recombinant, full-length
RT human claudin-1.";
RL PLoS ONE 8:E64517-E64517(2013).
RN [17]
RP INTERACTION WITH HCV HETERODIMER E1/E2 (MICROBIAL INFECTION), AND FUNCTION
RP (MICROBIAL INFECTION).
RX PubMed=24038151; DOI=10.1002/hep.26733;
RA Douam F., Dao Thi V.L., Maurin G., Fresquet J., Mompelat D., Zeisel M.B.,
RA Baumert T.F., Cosset F.L., Lavillette D.;
RT "Critical interaction between E1 and E2 glycoproteins determines binding
RT and fusion properties of hepatitis C virus during cell entry.";
RL Hepatology 59:776-788(2014).
CC -!- FUNCTION: Claudins function as major constituents of the tight junction
CC complexes that regulate the permeability of epithelia. While some
CC claudin family members play essential roles in the formation of
CC impermeable barriers, others mediate the permeability to ions and small
CC molecules. Often, several claudin family members are coexpressed and
CC interact with each other, and this determines the overall permeability.
CC CLDN1 is required to prevent the paracellular diffusion of small
CC molecules through tight junctions in the epidermis and is required for
CC the normal barrier function of the skin. Required for normal water
CC homeostasis and to prevent excessive water loss through the skin,
CC probably via an indirect effect on the expression levels of other
CC proteins, since CLDN1 itself seems to be dispensable for water barrier
CC formation in keratinocyte tight junctions (PubMed:23407391).
CC {ECO:0000269|PubMed:23407391}.
CC -!- FUNCTION: (Microbial infection) Acts as a co-receptor for hepatitis C
CC virus (HCV) in hepatocytes (PubMed:17325668, PubMed:20375010,
CC PubMed:24038151). Associates with CD81 and the CLDN1-CD81 receptor
CC complex is essential for HCV entry into host cell (PubMed:20375010).
CC Acts as a receptor for dengue virus (PubMed:24074594).
CC {ECO:0000269|PubMed:17325668, ECO:0000269|PubMed:20375010,
CC ECO:0000269|PubMed:24038151, ECO:0000269|PubMed:24074594}.
CC -!- SUBUNIT: Homopolymers interact with CLDN3, but not CLDN2, homopolymers.
CC Can form homo- and heteropolymers with other claudin family members
CC (PubMed:23704991). Directly interacts with TJP1/ZO-1, TJP2/ZO-2 and
CC TJP3/ZO-3. Interacts with MPDZ and PATJ (By similarity). Interacts with
CC OCLN, CLDN4, CLDN6 and CLDN9 (PubMed:20375010). Interacts with CD81
CC (PubMed:20375010, PubMed:21516087). {ECO:0000250|UniProtKB:O88551,
CC ECO:0000269|PubMed:20375010, ECO:0000269|PubMed:21516087,
CC ECO:0000269|PubMed:23704991}.
CC -!- SUBUNIT: (Microbial infection) Interacts with hepatitis c virus
CC heterodimer E1/E2. {ECO:0000269|PubMed:24038151}.
CC -!- SUBUNIT: (Microbial infection) Interacts with dengue virus small
CC envelope protein M. {ECO:0000269|PubMed:24074594}.
CC -!- INTERACTION:
CC O95832; Q07108: CD69; NbExp=3; IntAct=EBI-723889, EBI-2836595;
CC O95832; P11912: CD79A; NbExp=3; IntAct=EBI-723889, EBI-7797864;
CC O95832; Q8TBE3: FNDC9; NbExp=3; IntAct=EBI-723889, EBI-12142257;
CC O95832; Q96HJ5: MS4A3; NbExp=3; IntAct=EBI-723889, EBI-12806656;
CC O95832; Q7Z7N9: TMEM179B; NbExp=3; IntAct=EBI-723889, EBI-11724423;
CC O95832; Q9P0T7: TMEM9; NbExp=3; IntAct=EBI-723889, EBI-723976;
CC -!- SUBCELLULAR LOCATION: Cell junction, tight junction
CC {ECO:0000269|PubMed:20375010, ECO:0000269|PubMed:23407391}. Cell
CC membrane {ECO:0000269|PubMed:23704991}; Multi-pass membrane protein
CC {ECO:0000255}. Basolateral cell membrane {ECO:0000269|PubMed:20375010}.
CC Note=Associates with CD81 and the CLDN1-CD81 complex localizes to the
CC basolateral cell membrane. {ECO:0000269|PubMed:20375010}.
CC -!- TISSUE SPECIFICITY: Strongly expressed in liver and kidney. Expressed
CC in heart, brain, spleen, lung and testis. {ECO:0000269|PubMed:9931503}.
CC -!- DISEASE: Ichthyosis-sclerosing cholangitis neonatal syndrome (NISCH)
CC [MIM:607626]: A rare autosomal recessive complex ichthyosis syndrome
CC characterized by scalp hypotrichosis, scarring alopecia, mild diffuse
CC ichthyosis, sclerosing cholangitis and leukocyte vacuolization.
CC {ECO:0000269|PubMed:15521008, ECO:0000269|PubMed:16619213}. Note=The
CC disease is caused by variants affecting the gene represented in this
CC entry.
CC -!- SIMILARITY: Belongs to the claudin family. {ECO:0000305}.
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DR EMBL; AF101051; AAD16433.1; -; mRNA.
DR EMBL; AF115546; AAD22962.1; -; mRNA.
DR EMBL; AF134160; AAF61393.1; -; mRNA.
DR EMBL; AF260406; AAK20945.1; -; Genomic_DNA.
DR EMBL; AF260403; AAK20945.1; JOINED; Genomic_DNA.
DR EMBL; AF260404; AAK20945.1; JOINED; Genomic_DNA.
DR EMBL; AF260405; AAK20945.1; JOINED; Genomic_DNA.
DR EMBL; AY358652; AAQ89015.1; -; mRNA.
DR EMBL; CR457138; CAG33419.1; -; mRNA.
DR EMBL; BC012471; AAH12471.1; -; mRNA.
DR CCDS; CCDS3295.1; -.
DR RefSeq; NP_066924.1; NM_021101.4.
DR AlphaFoldDB; O95832; -.
DR SMR; O95832; -.
DR BioGRID; 114533; 23.
DR CORUM; O95832; -.
DR IntAct; O95832; 11.
DR MINT; O95832; -.
DR STRING; 9606.ENSP00000295522; -.
DR TCDB; 1.H.1.1.14; the claudin tight junction (claudin1) family.
DR GlyGen; O95832; 4 sites.
DR iPTMnet; O95832; -.
DR PhosphoSitePlus; O95832; -.
DR SwissPalm; O95832; -.
DR BioMuta; CLDN1; -.
DR EPD; O95832; -.
DR jPOST; O95832; -.
DR MassIVE; O95832; -.
DR MaxQB; O95832; -.
DR PaxDb; O95832; -.
DR PeptideAtlas; O95832; -.
DR PRIDE; O95832; -.
DR ProteomicsDB; 51077; -.
DR Antibodypedia; 3613; 816 antibodies from 43 providers.
DR DNASU; 9076; -.
DR Ensembl; ENST00000295522.4; ENSP00000295522.3; ENSG00000163347.6.
DR GeneID; 9076; -.
DR KEGG; hsa:9076; -.
DR MANE-Select; ENST00000295522.4; ENSP00000295522.3; NM_021101.5; NP_066924.1.
DR UCSC; uc003fsh.4; human.
DR CTD; 9076; -.
DR DisGeNET; 9076; -.
DR GeneCards; CLDN1; -.
DR HGNC; HGNC:2032; CLDN1.
DR HPA; ENSG00000163347; Tissue enhanced (liver, skin).
DR MalaCards; CLDN1; -.
DR MIM; 603718; gene.
DR MIM; 607626; phenotype.
DR neXtProt; NX_O95832; -.
DR OpenTargets; ENSG00000163347; -.
DR Orphanet; 59303; Neonatal ichthyosis-sclerosing cholangitis syndrome.
DR PharmGKB; PA26557; -.
DR VEuPathDB; HostDB:ENSG00000163347; -.
DR eggNOG; ENOG502R7HF; Eukaryota.
DR GeneTree; ENSGT00940000155387; -.
DR HOGENOM; CLU_076370_2_3_1; -.
DR InParanoid; O95832; -.
DR OMA; CCCPQKA; -.
DR OrthoDB; 1244077at2759; -.
DR PhylomeDB; O95832; -.
DR TreeFam; TF331936; -.
DR PathwayCommons; O95832; -.
DR Reactome; R-HSA-420029; Tight junction interactions.
DR SignaLink; O95832; -.
DR BioGRID-ORCS; 9076; 15 hits in 1073 CRISPR screens.
DR ChiTaRS; CLDN1; human.
DR GeneWiki; CLDN1; -.
DR GenomeRNAi; 9076; -.
DR Pharos; O95832; Tbio.
DR PRO; PR:O95832; -.
DR Proteomes; UP000005640; Chromosome 3.
DR RNAct; O95832; protein.
DR Bgee; ENSG00000163347; Expressed in upper leg skin and 139 other tissues.
DR ExpressionAtlas; O95832; baseline and differential.
DR Genevisible; O95832; HS.
DR GO; GO:0016324; C:apical plasma membrane; IEA:Ensembl.
DR GO; GO:0016323; C:basolateral plasma membrane; IDA:UniProtKB.
DR GO; GO:0005923; C:bicellular tight junction; IDA:UniProtKB.
DR GO; GO:0005737; C:cytoplasm; IEA:Ensembl.
DR GO; GO:0016021; C:integral component of membrane; TAS:ProtInc.
DR GO; GO:0005887; C:integral component of plasma membrane; IMP:UniProtKB.
DR GO; GO:0016328; C:lateral plasma membrane; IEA:Ensembl.
DR GO; GO:0005886; C:plasma membrane; IDA:ARUK-UCL.
DR GO; GO:0032991; C:protein-containing complex; IDA:UniProtKB.
DR GO; GO:0070160; C:tight junction; IDA:ARUK-UCL.
DR GO; GO:0042802; F:identical protein binding; IPI:UniProtKB.
DR GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR GO; GO:0001618; F:virus receptor activity; IMP:UniProtKB.
DR GO; GO:0007568; P:aging; IEA:Ensembl.
DR GO; GO:0070830; P:bicellular tight junction assembly; IMP:UniProtKB.
DR GO; GO:0016338; P:calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules; ISS:UniProtKB.
DR GO; GO:0007155; P:cell adhesion; IBA:GO_Central.
DR GO; GO:0034331; P:cell junction maintenance; ISS:ARUK-UCL.
DR GO; GO:0045216; P:cell-cell junction organization; IMP:MGI.
DR GO; GO:1903545; P:cellular response to butyrate; IEA:Ensembl.
DR GO; GO:0071346; P:cellular response to interferon-gamma; IEA:Ensembl.
DR GO; GO:0071284; P:cellular response to lead ion; IEA:Ensembl.
DR GO; GO:0071560; P:cellular response to transforming growth factor beta stimulus; IEA:Ensembl.
DR GO; GO:0071356; P:cellular response to tumor necrosis factor; IEA:Ensembl.
DR GO; GO:0008065; P:establishment of blood-nerve barrier; IEA:Ensembl.
DR GO; GO:0090557; P:establishment of endothelial intestinal barrier; IEA:Ensembl.
DR GO; GO:0061436; P:establishment of skin barrier; IMP:UniProtKB.
DR GO; GO:0042538; P:hyperosmotic salinity response; IEA:Ensembl.
DR GO; GO:0097421; P:liver regeneration; IEA:Ensembl.
DR GO; GO:0035633; P:maintenance of blood-brain barrier; NAS:ARUK-UCL.
DR GO; GO:1903348; P:positive regulation of bicellular tight junction assembly; IEA:Ensembl.
DR GO; GO:0030335; P:positive regulation of cell migration; IMP:ARUK-UCL.
DR GO; GO:0060054; P:positive regulation of epithelial cell proliferation involved in wound healing; IMP:ARUK-UCL.
DR GO; GO:0090303; P:positive regulation of wound healing; IMP:ARUK-UCL.
DR GO; GO:0051259; P:protein complex oligomerization; IDA:ARUK-UCL.
DR GO; GO:0071548; P:response to dexamethasone; IEA:Ensembl.
DR GO; GO:0045471; P:response to ethanol; IEA:Ensembl.
DR GO; GO:0070673; P:response to interleukin-18; IEA:Ensembl.
DR GO; GO:0032496; P:response to lipopolysaccharide; IEA:Ensembl.
DR GO; GO:0009636; P:response to toxic substance; IEA:Ensembl.
DR GO; GO:0061772; P:xenobiotic transport across blood-nerve barrier; IEA:Ensembl.
DR InterPro; IPR006187; Claudin.
DR InterPro; IPR003548; Claudin1.
DR InterPro; IPR017974; Claudin_CS.
DR InterPro; IPR004031; PMP22/EMP/MP20/Claudin.
DR PANTHER; PTHR12002; PTHR12002; 1.
DR PANTHER; PTHR12002:SF92; PTHR12002:SF92; 1.
DR Pfam; PF00822; PMP22_Claudin; 1.
DR PRINTS; PR01377; CLAUDIN1.
DR PROSITE; PS01346; CLAUDIN; 1.
PE 1: Evidence at protein level;
KW Cell junction; Cell membrane; Disulfide bond;
KW Host cell receptor for virus entry; Host-virus interaction; Ichthyosis;
KW Membrane; Receptor; Reference proteome; Tight junction; Transmembrane;
KW Transmembrane helix.
FT CHAIN 1..211
FT /note="Claudin-1"
FT /id="PRO_0000144729"
FT TOPO_DOM 1..7
FT /note="Cytoplasmic"
FT /evidence="ECO:0000250"
FT TRANSMEM 8..28
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 29..81
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 82..102
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 103..115
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 116..136
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 137..163
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 164..184
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 185..211
FT /note="Cytoplasmic"
FT /evidence="ECO:0000250"
FT REGION 192..211
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 210..211
FT /note="Interactions with TJP1, TJP2, TJP3 and PATJ"
FT /evidence="ECO:0000250"
FT DISULFID 54..64
FT /evidence="ECO:0000250"
FT MUTAGEN 32
FT /note="I->M: Loss of HCV receptor activity. Significant
FT loss of interaction with CD81. Reduced interaction with
FT OCLN."
FT /evidence="ECO:0000269|PubMed:17325668,
FT ECO:0000269|PubMed:20375010"
FT MUTAGEN 48
FT /note="E->K: Loss of HCV receptor activity. Significant
FT loss of interaction with CD81. Reduced interaction with
FT OCLN. According to PubMed:17325668 no effect observed on
FT HCV infection susceptibility in cell culture."
FT /evidence="ECO:0000269|PubMed:17325668,
FT ECO:0000269|PubMed:20375010"
FT CONFLICT 62
FT /note="I -> V (in Ref. 2; AAD22962)"
FT /evidence="ECO:0000305"
FT CONFLICT 135
FT /note="V -> A (in Ref. 2; AAD22962)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 211 AA; 22744 MW; 07269000E6C214F0 CRC64;
MANAGLQLLG FILAFLGWIG AIVSTALPQW RIYSYAGDNI VTAQAMYEGL WMSCVSQSTG
QIQCKVFDSL LNLSSTLQAT RALMVVGILL GVIAIFVATV GMKCMKCLED DEVQKMRMAV
IGGAIFLLAG LAILVATAWY GNRIVQEFYD PMTPVNARYE FGQALFTGWA AASLCLLGGA
LLCCSCPRKT TSYPTPRPYP KPAPSSGKDY V
//

3124
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ID LSHR_RAT Reviewed; 700 AA.
AC P16235; P70646; Q63807; Q63808; Q63809; Q6LDI7;
DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1990, sequence version 1.
DT 12-OCT-2022, entry version 184.
DE RecName: Full=Lutropin-choriogonadotropic hormone receptor;
DE Short=LH/CG-R;
DE AltName: Full=Luteinizing hormone receptor;
DE Short=LSH-R;
DE Flags: Precursor;
GN Name=Lhcgr;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=2502842; DOI=10.1126/science.2502842;
RA McFarland K.C., Sprengel R., Phillips H.S., Koehler M., Rosemblit N.,
RA Nikolics K., Segaloff D.L., Seeburg P.H.;
RT "Lutropin-choriogonadotropin receptor: an unusual member of the G protein-
RT coupled receptor family.";
RL Science 245:494-499(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE, AND ALTERNATIVE SPLICING.
RC STRAIN=Sprague-Dawley; TISSUE=Ovary;
RX PubMed=1353463; DOI=10.1016/0303-7207(92)90079-l;
RA Aatsinki J.T., Pietila E.M., Lakkakorpi J.T., Rajaniemi H.J.;
RT "Expression of the LH/CG receptor gene in rat ovarian tissue is regulated
RT by an extensive alternative splicing of the primary transcript.";
RL Mol. Cell. Endocrinol. 84:127-135(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2019252; DOI=10.1210/endo-128-5-2297;
RA Koo Y.B., Slaughter R.G., Ji T.H.;
RT "Structure of the luteinizing hormone receptor gene and multiple exons of
RT the coding sequence.";
RL Endocrinology 128:2297-2308(1991).
RN [4]
RP NUCLEOTIDE SEQUENCE, AND ALTERNATIVE SPLICING.
RX PubMed=1976554; DOI=10.1016/0303-7207(90)90034-6;
RA Bernard M.P., Myers R.V., Moyle W.R.;
RT "Cloning of rat lutropin (LH) receptor analogs lacking the soybean lectin
RT domain.";
RL Mol. Cell. Endocrinol. 71:R19-R23(1990).
RN [5]
RP NUCLEOTIDE SEQUENCE, AND ALTERNATIVE SPLICING.
RX PubMed=2281186; DOI=10.1016/b978-0-12-571146-3.50014-6;
RA Segaloff D.L., Sprengel R., Nikolics K., Ascoli M.;
RT "Structure of the lutropin/choriogonadotropin receptor.";
RL Recent Prog. Horm. Res. 46:261-301(1990).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-320.
RC TISSUE=Liver;
RX PubMed=2040640; DOI=10.1016/s0021-9258(18)99170-2;
RA Tsai-Morris C.H., Buczko E., Wang W., Xie X.-Z., Dufau M.L.;
RT "Structural organization of the rat luteinizing hormone (LH) receptor
RT gene.";
RL J. Biol. Chem. 266:11355-11359(1991).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 295-700.
RX PubMed=2174034; DOI=10.1016/s0021-9258(17)45380-4;
RA Tsai-Morris C.H., Buczko E., Wang W., Dufau M.L.;
RT "Intronic nature of the rat luteinizing hormone receptor gene defines a
RT soluble receptor subspecies with hormone binding activity.";
RL J. Biol. Chem. 265:19385-19388(1990).
RN [8]
RP PROTEIN SEQUENCE OF 27-44.
RX PubMed=2601325; DOI=10.1016/0022-4731(89)90482-2;
RA Dufau M.L., Minegishi T., Buczko E.S., Delgado C.J., Zhang R.;
RT "Characterization and structure of ovarian and testicular LH/hCG
RT receptors.";
RL J. Steroid Biochem. 33:715-720(1989).
RN [9]
RP PROTEIN SEQUENCE OF 27-37.
RX PubMed=2925659; DOI=10.1016/s0021-9258(18)83790-5;
RA Roche P.C., Ryan R.J.;
RT "Purification, characterization, and amino-terminal sequence of rat ovarian
RT receptor for luteinizing hormone/human choriogonadotropin.";
RL J. Biol. Chem. 264:4636-4641(1989).
RN [10]
RP MUTAGENESIS OF ASP-409; ASP-436; GLU-455 AND ASP-582.
RX PubMed=1714448; DOI=10.1016/s0021-9258(18)98570-4;
RA Ji I., Ji T.H.;
RT "Asp383 in the second transmembrane domain of the lutropin receptor is
RT important for high affinity hormone binding and cAMP production.";
RL J. Biol. Chem. 266:14953-14957(1991).
RN [11]
RP PALMITOYLATION AT CYS-647 AND CYS-648, AND MUTAGENESIS OF CYS-647 AND
RP CYS-648.
RX PubMed=7776964; DOI=10.1210/mend.9.2.7776964;
RA Zhu H., Wang H., Ascoli M.;
RT "The lutropin/choriogonadotropin receptor is palmitoylated at intracellular
RT cysteine residues.";
RL Mol. Endocrinol. 9:141-150(1995).
CC -!- FUNCTION: Receptor for lutropin-choriogonadotropic hormone. The
CC activity of this receptor is mediated by G proteins which activate
CC adenylate cyclase. {ECO:0000250|UniProtKB:P22888}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000250|UniProtKB:P22888};
CC Multi-pass membrane protein {ECO:0000250|UniProtKB:P22888}. Secreted.
CC Note=Some isoforms may be secreted.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=11;
CC Comment=Additional isoforms seem to exist.;
CC Name=1;
CC IsoId=P16235-1; Sequence=Displayed;
CC Name=1759;
CC IsoId=P16235-2; Sequence=VSP_001969, VSP_001977, VSP_001978;
CC Name=1834;
CC IsoId=P16235-3; Sequence=VSP_001977, VSP_001978;
CC Name=1950;
CC IsoId=P16235-4; Sequence=VSP_001968;
CC Name=2075;
CC IsoId=P16235-5; Sequence=VSP_001971, VSP_001973;
CC Name=C1;
CC IsoId=P16235-6; Sequence=VSP_001975, VSP_001976;
CC Name=C2;
CC IsoId=P16235-7; Sequence=VSP_001970;
CC Name=EA2;
CC IsoId=P16235-8; Sequence=VSP_001972;
CC Name=EB;
CC IsoId=P16235-9; Sequence=VSP_001972, VSP_001977, VSP_001978;
CC Name=B1;
CC IsoId=P16235-10; Sequence=VSP_001972, VSP_001974, VSP_001979;
CC Name=B3;
CC IsoId=P16235-11; Sequence=VSP_001974, VSP_001979;
CC -!- PTM: Sulfated. {ECO:0000250|UniProtKB:P22888}.
CC -!- SIMILARITY: Belongs to the G-protein coupled receptor 1 family.
CC FSH/LSH/TSH subfamily. {ECO:0000255|PROSITE-ProRule:PRU00521}.
CC -!- WEB RESOURCE: Name=Sequence-structure-function-analysis of glycoprotein
CC hormone receptors;
CC URL="http://www.ssfa-gphr.de/";
CC ---------------------------------------------------------------------------
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DR EMBL; M26199; AAA41528.1; -; mRNA.
DR EMBL; M61212; AAA41527.1; -; Genomic_DNA.
DR EMBL; M61211; AAA41527.1; JOINED; Genomic_DNA.
DR EMBL; S40803; AAB22680.1; -; Genomic_DNA.
DR EMBL; S40787; AAB22680.1; JOINED; Genomic_DNA.
DR EMBL; S40903; AAB22680.1; JOINED; Genomic_DNA.
DR EMBL; S40904; AAB22680.1; JOINED; Genomic_DNA.
DR EMBL; S40905; AAB22680.1; JOINED; Genomic_DNA.
DR EMBL; S40907; AAB22680.1; JOINED; Genomic_DNA.
DR EMBL; S40909; AAB22680.1; JOINED; Genomic_DNA.
DR EMBL; S40918; AAB22680.1; JOINED; Genomic_DNA.
DR EMBL; S40920; AAB22680.1; JOINED; Genomic_DNA.
DR EMBL; S40795; AAB22680.1; JOINED; Genomic_DNA.
DR EMBL; S40798; AAB22680.1; JOINED; Genomic_DNA.
DR EMBL; S40795; AAB22681.1; -; Genomic_DNA.
DR EMBL; S40787; AAB22681.1; JOINED; Genomic_DNA.
DR EMBL; S40903; AAB22681.1; JOINED; Genomic_DNA.
DR EMBL; S40904; AAB22681.1; JOINED; Genomic_DNA.
DR EMBL; S40905; AAB22681.1; JOINED; Genomic_DNA.
DR EMBL; S40907; AAB22681.1; JOINED; Genomic_DNA.
DR EMBL; S40909; AAB22681.1; JOINED; Genomic_DNA.
DR EMBL; S40918; AAB22681.1; JOINED; Genomic_DNA.
DR EMBL; S40920; AAB22681.1; JOINED; Genomic_DNA.
DR EMBL; S40803; AAB22682.2; -; Genomic_DNA.
DR EMBL; S40787; AAB22682.2; JOINED; Genomic_DNA.
DR EMBL; S40903; AAB22682.2; JOINED; Genomic_DNA.
DR EMBL; S40907; AAB22682.2; JOINED; Genomic_DNA.
DR EMBL; S40909; AAB22682.2; JOINED; Genomic_DNA.
DR EMBL; S40918; AAB22682.2; JOINED; Genomic_DNA.
DR EMBL; S40920; AAB22682.2; JOINED; Genomic_DNA.
DR EMBL; S40795; AAB22682.2; JOINED; Genomic_DNA.
DR EMBL; S40798; AAB22682.2; JOINED; Genomic_DNA.
DR EMBL; S40803; AAB22683.1; -; Genomic_DNA.
DR EMBL; S40787; AAB22683.1; JOINED; Genomic_DNA.
DR EMBL; S40903; AAB22683.1; JOINED; Genomic_DNA.
DR EMBL; S40904; AAB22683.1; JOINED; Genomic_DNA.
DR EMBL; S40905; AAB22683.1; JOINED; Genomic_DNA.
DR EMBL; S40907; AAB22683.1; JOINED; Genomic_DNA.
DR EMBL; S40909; AAB22683.1; JOINED; Genomic_DNA.
DR EMBL; S40918; AAB22683.1; JOINED; Genomic_DNA.
DR EMBL; S40920; AAB22683.1; JOINED; Genomic_DNA.
DR EMBL; S40795; AAB22683.1; JOINED; Genomic_DNA.
DR EMBL; S40798; AAB22683.1; JOINED; Genomic_DNA.
DR EMBL; S40803; AAB22684.2; -; Genomic_DNA.
DR EMBL; S40787; AAB22684.2; JOINED; Genomic_DNA.
DR EMBL; S40903; AAB22684.2; JOINED; Genomic_DNA.
DR EMBL; S40904; AAB22684.2; JOINED; Genomic_DNA.
DR EMBL; S40905; AAB22684.2; JOINED; Genomic_DNA.
DR EMBL; S40909; AAB22684.2; JOINED; Genomic_DNA.
DR EMBL; S40918; AAB22684.2; JOINED; Genomic_DNA.
DR EMBL; S40920; AAB22684.2; JOINED; Genomic_DNA.
DR EMBL; S40795; AAB22684.2; JOINED; Genomic_DNA.
DR EMBL; S40798; AAB22684.2; JOINED; Genomic_DNA.
DR EMBL; M68928; AAA41529.1; -; Genomic_DNA.
DR EMBL; M68917; AAA41529.1; JOINED; Genomic_DNA.
DR EMBL; M68918; AAA41529.1; JOINED; Genomic_DNA.
DR EMBL; M68919; AAA41529.1; JOINED; Genomic_DNA.
DR EMBL; M68920; AAA41529.1; JOINED; Genomic_DNA.
DR EMBL; M68921; AAA41529.1; JOINED; Genomic_DNA.
DR EMBL; M68922; AAA41529.1; JOINED; Genomic_DNA.
DR EMBL; M68923; AAA41529.1; JOINED; Genomic_DNA.
DR EMBL; M68925; AAA41529.1; JOINED; Genomic_DNA.
DR EMBL; M68926; AAA41529.1; JOINED; Genomic_DNA.
DR EMBL; M68927; AAA41529.1; JOINED; Genomic_DNA.
DR EMBL; AH004953; AAB42193.1; -; Genomic_DNA.
DR PIR; A49744; A49744.
DR PIR; I57668; I57668.
DR PIR; I77461; I77461.
DR RefSeq; NP_037110.1; NM_012978.1. [P16235-1]
DR AlphaFoldDB; P16235; -.
DR SMR; P16235; -.
DR STRING; 10116.ENSRNOP00000022481; -.
DR BindingDB; P16235; -.
DR ChEMBL; CHEMBL2456; -.
DR DrugCentral; P16235; -.
DR GlyGen; P16235; 6 sites.
DR iPTMnet; P16235; -.
DR PhosphoSitePlus; P16235; -.
DR SwissPalm; P16235; -.
DR PaxDb; P16235; -.
DR Ensembl; ENSRNOT00000022481; ENSRNOP00000022481; ENSRNOG00000016712. [P16235-1]
DR Ensembl; ENSRNOT00000096915; ENSRNOP00000089069; ENSRNOG00000016712. [P16235-2]
DR Ensembl; ENSRNOT00000098297; ENSRNOP00000079785; ENSRNOG00000016712. [P16235-8]
DR GeneID; 25477; -.
DR KEGG; rno:25477; -.
DR UCSC; RGD:3007; rat. [P16235-1]
DR CTD; 3973; -.
DR RGD; 3007; Lhcgr.
DR eggNOG; KOG2087; Eukaryota.
DR GeneTree; ENSGT00940000157364; -.
DR InParanoid; P16235; -.
DR OrthoDB; 257031at2759; -.
DR PhylomeDB; P16235; -.
DR Reactome; R-RNO-375281; Hormone ligand-binding receptors.
DR PRO; PR:P16235; -.
DR Proteomes; UP000002494; Chromosome 6.
DR GO; GO:0005737; C:cytoplasm; IDA:RGD.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:RGD.
DR GO; GO:0005768; C:endosome; IDA:RGD.
DR GO; GO:0005615; C:extracellular space; IDA:RGD.
DR GO; GO:0005887; C:integral component of plasma membrane; IDA:RGD.
DR GO; GO:0031233; C:intrinsic component of external side of plasma membrane; IDA:RGD.
DR GO; GO:0005764; C:lysosome; IDA:RGD.
DR GO; GO:0005634; C:nucleus; IDA:RGD.
DR GO; GO:0005886; C:plasma membrane; IDA:RGD.
DR GO; GO:0043235; C:receptor complex; IDA:RGD.
DR GO; GO:0051117; F:ATPase binding; IPI:RGD.
DR GO; GO:0038106; F:choriogonadotropin hormone binding; ISO:RGD.
DR GO; GO:0035472; F:choriogonadotropin hormone receptor activity; ISO:RGD.
DR GO; GO:0008528; F:G protein-coupled peptide receptor activity; IDA:RGD.
DR GO; GO:0042802; F:identical protein binding; IDA:RGD.
DR GO; GO:0004964; F:luteinizing hormone receptor activity; ISS:UniProtKB.
DR GO; GO:0017046; F:peptide hormone binding; IDA:RGD.
DR GO; GO:0007190; P:activation of adenylate cyclase activity; IDA:RGD.
DR GO; GO:0007189; P:adenylate cyclase-activating G protein-coupled receptor signaling pathway; ISO:RGD.
DR GO; GO:0007188; P:adenylate cyclase-modulating G protein-coupled receptor signaling pathway; IDA:RGD.
DR GO; GO:0050482; P:arachidonic acid secretion; IDA:RGD.
DR GO; GO:0071371; P:cellular response to gonadotropin stimulus; ISO:RGD.
DR GO; GO:0071373; P:cellular response to luteinizing hormone stimulus; ISS:UniProtKB.
DR GO; GO:0007417; P:central nervous system development; IEP:RGD.
DR GO; GO:0050890; P:cognition; ISO:RGD.
DR GO; GO:0046544; P:development of secondary male sexual characteristics; ISO:RGD.
DR GO; GO:0008585; P:female gonad development; ISO:RGD.
DR GO; GO:0007186; P:G protein-coupled receptor signaling pathway; ISO:RGD.
DR GO; GO:0009755; P:hormone-mediated signaling pathway; IDA:RGD.
DR GO; GO:0042700; P:luteinizing hormone signaling pathway; IDA:RGD.
DR GO; GO:0008584; P:male gonad development; ISO:RGD.
DR GO; GO:0001541; P:ovarian follicle development; ISO:RGD.
DR GO; GO:0022602; P:ovulation cycle process; ISO:RGD.
DR GO; GO:0007200; P:phospholipase C-activating G protein-coupled receptor signaling pathway; IDA:RGD.
DR GO; GO:0010524; P:positive regulation of calcium ion transport into cytosol; IDA:RGD.
DR GO; GO:0050850; P:positive regulation of calcium-mediated signaling; IDA:RGD.
DR GO; GO:0046886; P:positive regulation of hormone biosynthetic process; IDA:RGD.
DR GO; GO:0032962; P:positive regulation of inositol trisphosphate biosynthetic process; ISO:RGD.
DR GO; GO:0051281; P:positive regulation of release of sequestered calcium ion into cytosol; IDA:RGD.
DR GO; GO:0006622; P:protein targeting to lysosome; IMP:RGD.
DR GO; GO:0050810; P:regulation of steroid biosynthetic process; IEP:RGD.
DR GO; GO:0090030; P:regulation of steroid hormone biosynthetic process; ISO:RGD.
DR GO; GO:0034699; P:response to luteinizing hormone; IDA:CAFA.
DR GO; GO:0009410; P:response to xenobiotic stimulus; IEP:RGD.
DR GO; GO:0072520; P:seminiferous tubule development; ISO:RGD.
DR GO; GO:0007283; P:spermatogenesis; ISO:RGD.
DR GO; GO:0060065; P:uterus development; ISO:RGD.
DR Gene3D; 3.80.10.10; -; 1.
DR InterPro; IPR000276; GPCR_Rhodpsn.
DR InterPro; IPR017452; GPCR_Rhodpsn_7TM.
DR InterPro; IPR002131; Gphrmn_rcpt_fam.
DR InterPro; IPR026906; LRR_5.
DR InterPro; IPR032675; LRR_dom_sf.
DR InterPro; IPR002273; LSH_rcpt.
DR Pfam; PF00001; 7tm_1; 1.
DR Pfam; PF13306; LRR_5; 2.
DR PRINTS; PR00373; GLYCHORMONER.
DR PRINTS; PR00237; GPCRRHODOPSN.
DR PRINTS; PR01144; LSHRECEPTOR.
DR PROSITE; PS00237; G_PROTEIN_RECEP_F1_1; 1.
DR PROSITE; PS50262; G_PROTEIN_RECEP_F1_2; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cell membrane; Direct protein sequencing;
KW Disulfide bond; G-protein coupled receptor; Glycoprotein;
KW Leucine-rich repeat; Lipoprotein; Membrane; Palmitate; Receptor;
KW Reference proteome; Repeat; Secreted; Signal; Sulfation; Transducer;
KW Transmembrane; Transmembrane helix.
FT SIGNAL 1..26
FT /evidence="ECO:0000269|PubMed:2601325,
FT ECO:0000269|PubMed:2925659"
FT CHAIN 27..700
FT /note="Lutropin-choriogonadotropic hormone receptor"
FT /id="PRO_0000012783"
FT TOPO_DOM 27..362
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 363..390
FT /note="Helical; Name=1"
FT /evidence="ECO:0000255"
FT TOPO_DOM 391..399
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 400..422
FT /note="Helical; Name=2"
FT /evidence="ECO:0000255"
FT TOPO_DOM 423..443
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 444..466
FT /note="Helical; Name=3"
FT /evidence="ECO:0000255"
FT TOPO_DOM 467..486
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 487..509
FT /note="Helical; Name=4"
FT /evidence="ECO:0000255"
FT TOPO_DOM 510..529
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 530..551
FT /note="Helical; Name=5"
FT /evidence="ECO:0000255"
FT TOPO_DOM 552..574
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 575..598
FT /note="Helical; Name=6"
FT /evidence="ECO:0000255"
FT TOPO_DOM 599..609
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 610..631
FT /note="Helical; Name=7"
FT /evidence="ECO:0000255"
FT TOPO_DOM 632..700
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT REPEAT 126..150
FT /note="LRR 1"
FT REPEAT 152..175
FT /note="LRR 2"
FT REPEAT 176..200
FT /note="LRR 3"
FT REPEAT 202..224
FT /note="LRR 4"
FT REPEAT 225..248
FT /note="LRR 5"
FT REPEAT 250..271
FT /note="LRR 6"
FT MOD_RES 335
FT /note="Sulfotyrosine"
FT /evidence="ECO:0000250|UniProtKB:P22888"
FT LIPID 647
FT /note="S-palmitoyl cysteine"
FT /evidence="ECO:0000305|PubMed:7776964"
FT LIPID 648
FT /note="S-palmitoyl cysteine"
FT /evidence="ECO:0000305|PubMed:7776964"
FT CARBOHYD 103
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 178
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 199
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 295
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 303
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 317
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT DISULFID 443..518
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00521"
FT VAR_SEQ 83..132
FT /note="Missing (in isoform 1950)"
FT /evidence="ECO:0000305"
FT /id="VSP_001968"
FT VAR_SEQ 133..157
FT /note="Missing (in isoform 1759)"
FT /evidence="ECO:0000305"
FT /id="VSP_001969"
FT VAR_SEQ 184..700
FT /note="Missing (in isoform C2)"
FT /evidence="ECO:0000305"
FT /id="VSP_001970"
FT VAR_SEQ 232..293
FT /note="Missing (in isoform EA2, isoform EB and isoform B1)"
FT /evidence="ECO:0000305"
FT /id="VSP_001972"
FT VAR_SEQ 232..251
FT /note="DISSTKLQALPSHGLESIQT -> PCRATGWSPFRRSSPCLPTH (in
FT isoform 2075)"
FT /evidence="ECO:0000305"
FT /id="VSP_001971"
FT VAR_SEQ 252..700
FT /note="Missing (in isoform 2075)"
FT /evidence="ECO:0000305"
FT /id="VSP_001973"
FT VAR_SEQ 294..367
FT /note="QNFSFSIFENFSKQCESTVRKADNETLYSAIFEENELSGWDYDYGFCSPKTL
FT QCAPEPDAFNPCEDIMGYAFLR -> IFHFPFLKTSPNNAKAQLEKQITRRFIPPSLRR
FT MNSVAGIMIMASVHPRHSNVLQNQMLSTPVKILWAMPSLGS (in isoform B1
FT and isoform B3)"
FT /evidence="ECO:0000305"
FT /id="VSP_001974"
FT VAR_SEQ 294
FT /note="Q -> P (in isoform C1)"
FT /evidence="ECO:0000305"
FT /id="VSP_001975"
FT VAR_SEQ 295..700
FT /note="Missing (in isoform C1)"
FT /evidence="ECO:0000305"
FT /id="VSP_001976"
FT VAR_SEQ 321..342
FT /note="YSAIFEENELSGWDYDYGFCSP -> LHGALPAAHCLRGLPNKRPVL (in
FT isoform 1834, isoform 1759 and isoform EB)"
FT /evidence="ECO:0000305"
FT /id="VSP_001977"
FT VAR_SEQ 343..700
FT /note="Missing (in isoform 1834, isoform 1759 and isoform
FT EB)"
FT /evidence="ECO:0000305"
FT /id="VSP_001978"
FT VAR_SEQ 368..700
FT /note="Missing (in isoform B1 and isoform B3)"
FT /evidence="ECO:0000305"
FT /id="VSP_001979"
FT VARIANT 82
FT /note="I -> M (in isoform 1950)"
FT VARIANT 179
FT /note="E -> G (in isoform 1759)"
FT VARIANT 233
FT /note="I -> T (in isoform 1950)"
FT VARIANT 646
FT /note="G -> S (in isoform 1950)"
FT MUTAGEN 409
FT /note="D->N: Significant reduction of binding."
FT /evidence="ECO:0000269|PubMed:1714448"
FT MUTAGEN 436
FT /note="D->N: No change in binding or cAMP production."
FT /evidence="ECO:0000269|PubMed:1714448"
FT MUTAGEN 455
FT /note="E->Q: No change in binding or cAMP production."
FT /evidence="ECO:0000269|PubMed:1714448"
FT MUTAGEN 582
FT /note="D->N: No change in binding or cAMP production."
FT /evidence="ECO:0000269|PubMed:1714448"
FT MUTAGEN 647
FT /note="C->A: Trapped intracellularly and does not appear to
FT become mature; when associated with A-648."
FT /evidence="ECO:0000269|PubMed:7776964"
FT MUTAGEN 648
FT /note="C->A: Trapped intracellularly and does not appear to
FT become mature; when associated with A-647."
FT /evidence="ECO:0000269|PubMed:7776964"
FT CONFLICT 33
FT /note="R -> L (in Ref. 9; AA sequence)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 700 AA; 78036 MW; 31807E73BAC94F1F CRC64;
MGRRVPALRQ LLVLAVLLLK PSQLQSRELS GSRCPEPCDC APDGALRCPG PRAGLARLSL
TYLPVKVIPS QAFRGLNEVV KIEISQSDSL ERIEANAFDN LLNLSELLIQ NTKNLLYIEP
GAFTNLPRLK YLSICNTGIR TLPDVTKISS SEFNFILEIC DNLHITTIPG NAFQGMNNES
VTLKLYGNGF EEVQSHAFNG TTLISLELKE NIYLEKMHSG AFQGATGPSI LDISSTKLQA
LPSHGLESIQ TLIALSSYSL KTLPSKEKFT SLLVATLTYP SHCCAFRNLP KKEQNFSFSI
FENFSKQCES TVRKADNETL YSAIFEENEL SGWDYDYGFC SPKTLQCAPE PDAFNPCEDI
MGYAFLRVLI WLINILAIFG NLTVLFVLLT SRYKLTVPRF LMCNLSFADF CMGLYLLLIA
SVDSQTKGQY YNHAIDWQTG SGCGAAGFFT VFASELSVYT LTVITLERWH TITYAVQLDQ
KLRLRHAIPI MLGGWLFSTL IATMPLVGIS NYMKVSICLP MDVESTLSQV YILSILILNV
VAFVVICACY IRIYFAVQNP ELTAPNKDTK IAKKMAILIF TDFTCMAPIS FFAISAAFKV
PLITVTNSKI LLVLFYPVNS CANPFLYAIF TKAFQRDFLL LLSRFGCCKR RAELYRRKEF
SAYTSNCKNG FPGASKPSQA TLKLSTVHCQ QPIPPRALTH
//

85
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ID TCMO_STRGA Reviewed; 339 AA.
AC P39896;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 75.
DE RecName: Full=Tetracenomycin polyketide synthesis 8-O-methyl transferase TcmO;
DE EC=2.1.1.-;
GN Name=tcmO;
OS Streptomyces glaucescens.
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces.
OX NCBI_TaxID=1907;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=DSM 40716 / ETH 22794 / Tue 49;
RX PubMed=1548230; DOI=10.1128/jb.174.6.1810-1820.1992;
RA Summers R.G., Wendt-Pienkowski E., Motamedi H., Hutchinson C.R.;
RT "Nucleotide sequence of the tcmII-tcmIV region of the tetracenomycin C
RT biosynthetic gene cluster of Streptomyces glaucescens and evidence that the
RT tcmN gene encodes a multifunctional cyclase-dehydratase-O-methyl
RT transferase.";
RL J. Bacteriol. 174:1810-1820(1992).
CC -!- PATHWAY: Antibiotic biosynthesis; tetracenomycin C biosynthesis.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. Cation-independent O-methyltransferase family.
CC {ECO:0000255|PROSITE-ProRule:PRU01020}.
CC ---------------------------------------------------------------------------
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DR EMBL; M80674; AAA67519.1; -; Genomic_DNA.
DR PIR; C42276; C42276.
DR RefSeq; WP_043504920.1; NZ_CP009438.1.
DR AlphaFoldDB; P39896; -.
DR SMR; P39896; -.
DR STRING; 1907.SGLAU_26375; -.
DR eggNOG; COG2345; Bacteria.
DR OMA; NTNHGEL; -.
DR OrthoDB; 1213908at2; -.
DR BioCyc; MetaCyc:MON-18605; -.
DR UniPathway; UPA00174; -.
DR GO; GO:0008171; F:O-methyltransferase activity; IEA:InterPro.
DR GO; GO:0017000; P:antibiotic biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR Gene3D; 1.10.10.10; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR031725; ASMT_dimerisation.
DR InterPro; IPR016461; COMT-like.
DR InterPro; IPR001077; O_MeTrfase_dom.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR PANTHER; PTHR11746; PTHR11746; 1.
DR Pfam; PF16864; Dimerisation2; 1.
DR Pfam; PF00891; Methyltransf_2; 1.
DR PIRSF; PIRSF005739; O-mtase; 1.
DR SUPFAM; SSF46785; SSF46785; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51683; SAM_OMT_II; 1.
PE 3: Inferred from homology;
KW Antibiotic biosynthesis; Methyltransferase; S-adenosyl-L-methionine;
KW Transferase.
FT CHAIN 1..339
FT /note="Tetracenomycin polyketide synthesis 8-O-methyl
FT transferase TcmO"
FT /id="PRO_0000072457"
FT ACT_SITE 246
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01020"
FT BINDING 200
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01020"
FT BINDING 226..228
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01020"
SQ SEQUENCE 339 AA; 37035 MW; B228B66B24217F80 CRC64;
MTPHTHVRGP GDILQLTMAF YGSRALISAV ELDLFTLLAG KPLPLGELCE RAGIHPRGAR
DFLDALVALG LLEREGEDTY RNSPAADRHL DRRKPGYVGG YARLADTKLF PVWARLTEAL
RTGEKQVPSQ GGFFGGYADP EAARGFLGAM DAVNGGVGHS LAGALDWTEY SSFVDLGGAR
GNLAAHLHRA HPHLRATCFD LPEMEPFFQE HMKSLETTDQ VRFAGGDFFT DPLPRADVFI
VGHILHYFGL RQREALIARI HQALTPGGAV LVYDRMIDDD RRSAALSLLG SLNMLLTSDE
GREYTPAECV RWLSDAGFTD VRTTAVSGPD TLAIGRKPR
//

381
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ID DNJC5_MOUSE Reviewed; 198 AA.
AC P60904; P54101;
DT 13-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT 13-APR-2004, sequence version 1.
DT 12-OCT-2022, entry version 158.
DE RecName: Full=DnaJ homolog subfamily C member 5 {ECO:0000305};
DE AltName: Full=Cysteine string protein {ECO:0000250|UniProtKB:Q9H3Z4};
DE Short=CSP {ECO:0000250|UniProtKB:Q9H3Z4};
DE AltName: Full=Cysteine-string protein isoform alpha {ECO:0000303|PubMed:20847230};
GN Name=Dnajc5 {ECO:0000312|MGI:MGI:892995};
GN Synonyms=Cspalpha {ECO:0000303|PubMed:20847230};
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Brain;
RA Qin N., Lin T., Birnbaumer L.;
RL Submitted (OCT-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J; TISSUE=Olfactory bulb, and Skin;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [3]
RP PROTEIN SEQUENCE OF 8-24 AND 42-72, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=C57BL/6J; TISSUE=Brain;
RA Lubec G., Kang S.U.;
RL Submitted (APR-2007) to UniProtKB.
RN [4]
RP INTERACTION WITH HSC70 AND SGTA, SUBCELLULAR LOCATION, PALMITOYLATION, AND
RP MUTAGENESIS OF CYS-113; CYS-118; CYS-121; PHE-129 AND LYS-135.
RX PubMed=17034881; DOI=10.1016/j.bbamcr.2006.08.054;
RA Boal F., Le Pevelen S., Cziepluch C., Scotti P., Lang J.;
RT "Cysteine-string protein isoform beta (Cspbeta) is targeted to the trans-
RT Golgi network as a non-palmitoylated CSP in clonal beta-cells.";
RL Biochim. Biophys. Acta 1773:109-119(2007).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=17208939; DOI=10.1074/mcp.m600218-mcp200;
RA Lee J., Xu Y., Chen Y., Sprung R., Kim S.C., Xie S., Zhao Y.;
RT "Mitochondrial phosphoproteome revealed by an improved IMAC method and
RT MS/MS/MS.";
RL Mol. Cell. Proteomics 6:669-676(2007).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=17242355; DOI=10.1073/pnas.0609836104;
RA Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.;
RT "Large-scale phosphorylation analysis of mouse liver.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=18630941; DOI=10.1021/pr800223m;
RA Zhou H., Ye M., Dong J., Han G., Jiang X., Wu R., Zou H.;
RT "Specific phosphopeptide enrichment with immobilized titanium ion affinity
RT chromatography adsorbent for phosphoproteome analysis.";
RL J. Proteome Res. 7:3957-3967(2008).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19144319; DOI=10.1016/j.immuni.2008.11.006;
RA Trost M., English L., Lemieux S., Courcelles M., Desjardins M.,
RA Thibault P.;
RT "The phagosomal proteome in interferon-gamma-activated macrophages.";
RL Immunity 30:143-154(2009).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-10, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Embryonic fibroblast;
RX PubMed=19131326; DOI=10.1074/mcp.m800451-mcp200;
RA Sweet S.M., Bailey C.M., Cunningham D.L., Heath J.K., Cooper H.J.;
RT "Large scale localization of protein phosphorylation by use of electron
RT capture dissociation mass spectrometry.";
RL Mol. Cell. Proteomics 8:904-912(2009).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-15 AND SER-151, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung,
RC Pancreas, Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [11]
RP FUNCTION, INTERACTION WITH SYT1; SYT5; SYT7; SYT9 AND HSC70, MUTAGENESIS OF
RP SER-10 AND GLU-93, AND PHOSPHORYLATION AT SER-10.
RX PubMed=20847230; DOI=10.1096/fj.09-152033;
RA Boal F., Laguerre M., Milochau A., Lang J., Scotti P.A.;
RT "A charged prominence in the linker domain of the cysteine-string protein
RT Cspalpha mediates its regulated interaction with the calcium sensor
RT synaptotagmin 9 during exocytosis.";
RL FASEB J. 25:132-143(2011).
RN [12]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=22187053; DOI=10.1038/emboj.2011.467;
RA Sharma M., Burre J., Bronk P., Zhang Y., Xu W., Suedhof T.C.;
RT "CSPalpha knockout causes neurodegeneration by impairing SNAP-25
RT function.";
RL EMBO J. 31:829-841(2012).
RN [13]
RP INTERACTION WITH ZDHHC13 AND ZDHHC17.
RX PubMed=25253725; DOI=10.1091/mbc.e14-06-1169;
RA Lemonidis K., Gorleku O.A., Sanchez-Perez M.C., Grefen C.,
RA Chamberlain L.H.;
RT "The Golgi S-acylation machinery comprises zDHHC enzymes with major
RT differences in substrate affinity and S-acylation activity.";
RL Mol. Biol. Cell 25:3870-3883(2014).
RN [14]
RP INTERACTION WITH ZDHHC17 AND ZDHHC13.
RX PubMed=26198635; DOI=10.1074/jbc.m115.657668;
RA Lemonidis K., Sanchez-Perez M.C., Chamberlain L.H.;
RT "Identification of a novel sequence motif recognized by the ankyrin repeat
RT domain of zDHHC17/13 S-acyltransferases.";
RL J. Biol. Chem. 290:21939-21950(2015).
RN [15]
RP REVIEW.
RX PubMed=25800794; DOI=10.1016/j.semcdb.2015.03.008;
RA Burgoyne R.D., Morgan A.;
RT "Cysteine string protein (CSP) and its role in preventing
RT neurodegeneration.";
RL Semin. Cell Dev. Biol. 40:153-159(2015).
RN [16]
RP STRUCTURE BY NMR OF 5-100.
RG RIKEN structural genomics initiative (RSGI);
RT "Solution structure of J-domain from mouse DnaJ subfamily C member 5.";
RL Submitted (NOV-2005) to the PDB data bank.
CC -!- FUNCTION: Acts as a co-chaperone for the SNARE protein SNAP-25
CC (PubMed:22187053). Involved in the calcium-mediated control of a late
CC stage of exocytosis (PubMed:20847230). Acts as a general chaperone in
CC regulated exocytosis (By similarity). May have an important role in
CC presynaptic function (By similarity). May be involved in calcium-
CC dependent neurotransmitter release at nerve endings (By similarity).
CC {ECO:0000250|UniProtKB:Q29455, ECO:0000269|PubMed:20847230,
CC ECO:0000269|PubMed:22187053}.
CC -!- SUBUNIT: Homodimer (Probable). Interacts with the chaperone complex
CC consisting of HSC70 and SGTA (PubMed:17034881, PubMed:20847230).
CC Interacts with ZDHHC13 (via ANK repeats) (PubMed:25253725,
CC PubMed:26198635). Interacts with ZDHHC17 (via ANK repeats)
CC (PubMed:25253725, PubMed:26198635). Interacts with SYT1, SYT5 and SYT7,
CC and with SYT9, forming a complex with SNAP25 (PubMed:20847230). The
CC interaction with SYT9 is stimulated tenfold in presence of calcium
CC (PubMed:20847230). {ECO:0000269|PubMed:17034881,
CC ECO:0000269|PubMed:20847230, ECO:0000269|PubMed:25253725,
CC ECO:0000269|PubMed:26198635, ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol
CC {ECO:0000250|UniProtKB:Q29455}. Membrane {ECO:0000269|PubMed:17034881};
CC Lipid-anchor {ECO:0000269|PubMed:17034881}. Cytoplasmic vesicle,
CC secretory vesicle, chromaffin granule membrane
CC {ECO:0000250|UniProtKB:Q29455}. Melanosome
CC {ECO:0000250|UniProtKB:Q9H3Z4}. Cell membrane
CC {ECO:0000250|UniProtKB:Q9H3Z4}. Note=The association with membranes is
CC regulated by palmitoylation (By similarity). Colocalizes with insulin
CC granules, when overexpressed in an islet cell line (PubMed:17034881).
CC {ECO:0000250|UniProtKB:Q29455, ECO:0000269|PubMed:17034881}.
CC -!- PTM: Formation of the chaperone complex DNAJC5/HSC70 is not regulated
CC by phosphorylation (PubMed:20847230). Ser-10 phosphorylation induces an
CC order-to-disorder transition triggering the interaction with Lys-58 (By
CC similarity). This conformational switch modulates DNAJC5's cellular
CC functions by reducing binding to syntaxin and synaptogamin without
CC altering HSC70 interactions (By similarity).
CC {ECO:0000250|UniProtKB:Q9H3Z4, ECO:0000269|PubMed:20847230}.
CC -!- PTM: Palmitoylated (PubMed:17034881). Could be palmitoylated by DHHC3,
CC DHHC7, DHHC15 and DHHC17 (By similarity). Palmitoylation occurs
CC probably in the cysteine-rich domain and regulates DNAJC5 membrane
CC attachment (PubMed:17034881). {ECO:0000250|UniProtKB:Q29455,
CC ECO:0000269|PubMed:17034881}.
CC -!- DISRUPTION PHENOTYPE: Defective SNAP-25 function, which causes
CC neurodegeneration by impairing SNARE-complex assembly
CC (PubMed:22187053). {ECO:0000269|PubMed:22187053}.
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DR EMBL; AF032115; AAB87080.1; -; mRNA.
DR EMBL; AK029006; BAC26236.1; -; mRNA.
DR EMBL; AK032373; BAC27841.1; -; mRNA.
DR CCDS; CCDS17215.1; -.
DR RefSeq; NP_001258513.1; NM_001271584.1.
DR RefSeq; NP_001258514.1; NM_001271585.1.
DR RefSeq; NP_058055.1; NM_016775.3.
DR RefSeq; XP_011238225.1; XM_011239923.2.
DR PDB; 2CTW; NMR; -; A=5-100.
DR PDBsum; 2CTW; -.
DR AlphaFoldDB; P60904; -.
DR SMR; P60904; -.
DR BioGRID; 198948; 7.
DR CORUM; P60904; -.
DR IntAct; P60904; 7.
DR MINT; P60904; -.
DR STRING; 10090.ENSMUSP00000072175; -.
DR TCDB; 8.A.192.1.1; the dnaj homolog (dnaj) family.
DR iPTMnet; P60904; -.
DR PhosphoSitePlus; P60904; -.
DR SwissPalm; P60904; -.
DR EPD; P60904; -.
DR jPOST; P60904; -.
DR MaxQB; P60904; -.
DR PaxDb; P60904; -.
DR PeptideAtlas; P60904; -.
DR PRIDE; P60904; -.
DR ProteomicsDB; 277354; -.
DR Antibodypedia; 2284; 255 antibodies from 32 providers.
DR DNASU; 13002; -.
DR Ensembl; ENSMUST00000072334; ENSMUSP00000072175; ENSMUSG00000000826.
DR Ensembl; ENSMUST00000108796; ENSMUSP00000104424; ENSMUSG00000000826.
DR Ensembl; ENSMUST00000108797; ENSMUSP00000104425; ENSMUSG00000000826.
DR GeneID; 13002; -.
DR KEGG; mmu:13002; -.
DR UCSC; uc008omp.2; mouse.
DR CTD; 80331; -.
DR MGI; MGI:892995; Dnajc5.
DR VEuPathDB; HostDB:ENSMUSG00000000826; -.
DR eggNOG; KOG0716; Eukaryota.
DR GeneTree; ENSGT00940000155597; -.
DR InParanoid; P60904; -.
DR OMA; CKPRPRD; -.
DR OrthoDB; 1401920at2759; -.
DR PhylomeDB; P60904; -.
DR TreeFam; TF105164; -.
DR Reactome; R-MMU-6798695; Neutrophil degranulation.
DR Reactome; R-MMU-888590; GABA synthesis, release, reuptake and degradation.
DR BioGRID-ORCS; 13002; 2 hits in 74 CRISPR screens.
DR ChiTaRS; Dnajc5; mouse.
DR EvolutionaryTrace; P60904; -.
DR PRO; PR:P60904; -.
DR Proteomes; UP000000589; Chromosome 2.
DR RNAct; P60904; protein.
DR Bgee; ENSMUSG00000000826; Expressed in barrel cortex and 253 other tissues.
DR ExpressionAtlas; P60904; baseline and differential.
DR Genevisible; P60904; MM.
DR GO; GO:0031225; C:anchored component of membrane; ISS:UniProtKB.
DR GO; GO:0098993; C:anchored component of synaptic vesicle membrane; ISO:MGI.
DR GO; GO:0042584; C:chromaffin granule membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0060203; C:clathrin-sculpted glutamate transport vesicle membrane; TAS:Reactome.
DR GO; GO:0005829; C:cytosol; ISS:UniProtKB.
DR GO; GO:0005794; C:Golgi apparatus; ISO:MGI.
DR GO; GO:0043231; C:intracellular membrane-bounded organelle; ISO:MGI.
DR GO; GO:0042470; C:melanosome; IEA:UniProtKB-SubCell.
DR GO; GO:0016020; C:membrane; IBA:GO_Central.
DR GO; GO:0031594; C:neuromuscular junction; IDA:SynGO.
DR GO; GO:0005886; C:plasma membrane; ISS:UniProtKB.
DR GO; GO:0098793; C:presynapse; IDA:SynGO.
DR GO; GO:0008021; C:synaptic vesicle; IDA:MGI.
DR GO; GO:0043008; F:ATP-dependent protein binding; ISO:MGI.
DR GO; GO:0061077; P:chaperone-mediated protein folding; IDA:SynGO.
DR GO; GO:0043524; P:negative regulation of neuron apoptotic process; IGI:MGI.
DR GO; GO:0051402; P:neuron apoptotic process; IGI:MGI.
DR GO; GO:0098693; P:regulation of synaptic vesicle cycle; IDA:SynGO.
DR CDD; cd06257; DnaJ; 1.
DR Gene3D; 1.10.287.110; -; 1.
DR InterPro; IPR001623; DnaJ_domain.
DR InterPro; IPR018253; DnaJ_domain_CS.
DR InterPro; IPR036869; J_dom_sf.
DR Pfam; PF00226; DnaJ; 1.
DR PRINTS; PR00625; JDOMAIN.
DR SMART; SM00271; DnaJ; 1.
DR SUPFAM; SSF46565; SSF46565; 1.
DR PROSITE; PS00636; DNAJ_1; 1.
DR PROSITE; PS50076; DNAJ_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cell membrane; Chaperone; Cytoplasm;
KW Cytoplasmic vesicle; Direct protein sequencing; Lipoprotein; Membrane;
KW Palmitate; Phosphoprotein; Reference proteome.
FT CHAIN 1..198
FT /note="DnaJ homolog subfamily C member 5"
FT /id="PRO_0000071053"
FT DOMAIN 13..82
FT /note="J"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00286"
FT MOD_RES 8
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9H3Z4"
FT MOD_RES 10
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19131326"
FT MOD_RES 12
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9H3Z4"
FT MOD_RES 15
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 17
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000250|UniProtKB:Q9H3Z4"
FT MOD_RES 56
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9H3Z4"
FT MOD_RES 151
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MUTAGEN 10
FT /note="S->D: Reduced interaction with SYT9, but no effect
FT on the interaction with HSC70."
FT /evidence="ECO:0000269|PubMed:20847230"
FT MUTAGEN 93
FT /note="E->V: Reduced interaction with SYT9."
FT /evidence="ECO:0000269|PubMed:20847230"
FT MUTAGEN 113
FT /note="C->V: No effect on palmitoylation. No change in
FT subcellular location; when associated with G-118 and
FT F-121."
FT /evidence="ECO:0000269|PubMed:17034881"
FT MUTAGEN 118
FT /note="C->G: No effect on palmitoylation. No change in
FT subcellular location; when associated with V-113 and
FT F-121."
FT /evidence="ECO:0000269|PubMed:17034881"
FT MUTAGEN 121
FT /note="C->F: No effect on palmitoylation. No change in
FT subcellular location; when associated with V-113 and
FT G-118."
FT /evidence="ECO:0000269|PubMed:17034881"
FT MUTAGEN 129
FT /note="F->C: No effect on palmitoylation. No change in
FT subcellular location; when associated with H-135."
FT /evidence="ECO:0000269|PubMed:17034881"
FT MUTAGEN 135
FT /note="K->H: No effect on palmitoylation. No change in
FT subcellular location; when associated with C-129."
FT /evidence="ECO:0000269|PubMed:17034881"
FT HELIX 16..20
FT /evidence="ECO:0007829|PDB:2CTW"
FT HELIX 28..41
FT /evidence="ECO:0007829|PDB:2CTW"
FT TURN 44..46
FT /evidence="ECO:0007829|PDB:2CTW"
FT HELIX 51..67
FT /evidence="ECO:0007829|PDB:2CTW"
FT HELIX 70..78
FT /evidence="ECO:0007829|PDB:2CTW"
FT HELIX 81..89
FT /evidence="ECO:0007829|PDB:2CTW"
FT HELIX 94..100
FT /evidence="ECO:0007829|PDB:2CTW"
SQ SEQUENCE 198 AA; 22101 MW; 52F98261FBAD978F CRC64;
MADQRQRSLS TSGESLYHVL GLDKNATSDD IKKSYRKLAL KYHPDKNPDN PEAADKFKEI
NNAHAILTDA TKRNIYDKYG SLGLYVAEQF GEENVNTYFV LSSWWAKALF VVCGLLTCCY
CCCCLCCCFN CCCGKCKPKA PEGEETEFYV SPEDLEAQLQ SDEREATDTP IVIQPASATE
TTQLTADSHP SYHTDGFN
//

790
Tests/SwissProt/P62258.txt Normal file
View File

@ -0,0 +1,790 @@
ID 1433E_HUMAN Reviewed; 255 AA.
AC P62258; B3KY71; D3DTH5; P29360; P42655; Q4VJB6; Q53XZ5; Q63631; Q7M4R4;
DT 05-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 12-OCT-2022, entry version 198.
DE RecName: Full=14-3-3 protein epsilon;
DE Short=14-3-3E;
GN Name=YWHAE;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RX PubMed=7644510; DOI=10.1073/pnas.92.17.7892;
RA Conklin D.S., Galaktionov K., Beach D.;
RT "14-3-3 proteins associate with cdc25 phosphatases.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:7892-7896(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RC TISSUE=Liver;
RX PubMed=8858348; DOI=10.1101/gr.6.8.735;
RA Chong S.S., Tanigami A., Roschke A.V., Ledbetter D.H.;
RT "14-3-3 epsilon has no homology to LIS1 and lies telomeric to it on
RT chromosome 17p13.3 outside the Miller-Dieker syndrome chromosome region.";
RL Genome Res. 6:735-741(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RX PubMed=8684458; DOI=10.1038/382308a0;
RA Jin D.-Y., Lyu M.S., Kozak C.A., Jeang K.-T.;
RT "Function of 14-3-3 proteins.";
RL Nature 382:308-308(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM SV), AND ALTERNATIVE SPLICING.
RC TISSUE=Brain;
RX PubMed=20417184; DOI=10.1016/j.bbrc.2010.04.104;
RA Han D., Ye G., Liu T., Chen C., Yang X., Wan B., Pan Y., Yu L.;
RT "Functional identification of a novel 14-3-3 epsilon splicing variant
RT suggests dimerization is not necessary for 14-3-3 epsilon to inhibit UV-
RT induced apoptosis.";
RL Biochem. Biophys. Res. Commun. 396:401-406(2010).
RN [5]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RC TISSUE=Heart;
RA Luk S.C.W., Lee C.Y., Waye M.M.Y.;
RT "Sequence determination of human epsilon 14-3-3 protein.";
RL Submitted (JUN-1995) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Tanigami A., Chong S.S., Ledbetter D.H.;
RT "14-3-3 epsilon genomic sequence.";
RL Submitted (AUG-1998) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND SV).
RC TISSUE=Caudate nucleus, Heart, and Subthalamic nucleus;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [8]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S.,
RA Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y.,
RA Phelan M., Farmer A.;
RT "Cloning of human full-length CDSs in BD Creator(TM) system donor vector.";
RL Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.
RN [9]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [10]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Placenta;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [11]
RP PROTEIN SEQUENCE OF 1-19.
RC TISSUE=Platelet;
RX PubMed=12665801; DOI=10.1038/nbt810;
RA Gevaert K., Goethals M., Martens L., Van Damme J., Staes A., Thomas G.R.,
RA Vandekerckhove J.;
RT "Exploring proteomes and analyzing protein processing by mass spectrometric
RT identification of sorted N-terminal peptides.";
RL Nat. Biotechnol. 21:566-569(2003).
RN [12]
RP PROTEIN SEQUENCE OF 1-56; 62-73; 95-118; 131-193 AND 197-255, INTERACTION
RP WITH PI4KB; TBC1D22A AND TBC1D22B, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=23572552; DOI=10.1128/mbio.00098-13;
RA Greninger A.L., Knudsen G.M., Betegon M., Burlingame A.L., DeRisi J.L.;
RT "ACBD3 interaction with TBC1 domain 22 protein is differentially affected
RT by enteroviral and kobuviral 3A protein binding.";
RL MBio 4:E00098-E00098(2013).
RN [13]
RP PROTEIN SEQUENCE OF 1-19; 30-50 AND 131-170, ACETYLATION AT MET-1, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC TISSUE=B-cell lymphoma;
RA Bienvenut W.V.;
RL Submitted (MAY-2005) to UniProtKB.
RN [14]
RP PROTEIN SEQUENCE OF 50-60, AND INTERACTION WITH KSR1.
RX PubMed=10409742; DOI=10.1128/mcb.19.8.5523;
RA Stewart S., Sundaram M., Zhang Y., Lee J., Han M., Guan K.L.;
RT "Kinase suppressor of Ras forms a multiprotein signaling complex and
RT modulates MEK localization.";
RL Mol. Cell. Biol. 19:5523-5534(1999).
RN [15]
RP PROTEIN SEQUENCE OF 103-108; 120-123; 131-141 AND 143-153.
RC TISSUE=Histiocytic lymphoma;
RX PubMed=2026444;
RA Demeter J., Medzihradszky D., Kha H., Goetzl E.J., Turck C.W.;
RT "Isolation and partial characterization of the structures of fibroblast
RT activating factor-related proteins from U937 cells.";
RL Immunology 72:350-354(1991).
RN [16]
RP PROTEIN SEQUENCE OF 131-141 AND 154-190, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC TISSUE=Brain, and Cajal-Retzius cell;
RA Lubec G., Afjehi-Sadat L.;
RL Submitted (MAR-2007) to UniProtKB.
RN [17]
RP INTERACTION WITH HCV CORE PROTEIN (MICROBIAL INFECTION).
RX PubMed=10644344; DOI=10.1128/jvi.74.4.1736-1741.2000;
RA Aoki H., Hayashi J., Moriyama M., Arakawa Y., Hino O.;
RT "Hepatitis C virus core protein interacts with 14-3-3 protein and activates
RT the kinase Raf-1.";
RL J. Virol. 74:1736-1741(2000).
RN [18]
RP INTERACTION WITH AANAT.
RX PubMed=11427721; DOI=10.1073/pnas.141118798;
RA Ganguly S., Gastel J.A., Weller J.L., Schwartz C., Jaffe H.,
RA Namboodiri M.A., Coon S.L., Hickman A.B., Rollag M., Obsil T.,
RA Beauverger P., Ferry G., Boutin J.A., Klein D.C.;
RT "Role of a pineal cAMP-operated arylalkylamine N-acetyltransferase/14-3-3-
RT binding switch in melatonin synthesis.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:8083-8088(2001).
RN [19]
RP INTERACTION WITH CDKN1B, AND SUBCELLULAR LOCATION.
RX PubMed=12042314; DOI=10.1074/jbc.m203668200;
RA Fujita N., Sato S., Katayama K., Tsuruo T.;
RT "Akt-dependent phosphorylation of p27Kip1 promotes binding to 14-3-3 and
RT cytoplasmic localization.";
RL J. Biol. Chem. 277:28706-28713(2002).
RN [20]
RP FUNCTION, INTERACTION WITH HSF1, AND SUBCELLULAR LOCATION.
RX PubMed=12917326; DOI=10.1128/mcb.23.17.6013-6026.2003;
RA Wang X., Grammatikakis N., Siganou A., Calderwood S.K.;
RT "Regulation of molecular chaperone gene transcription involves the serine
RT phosphorylation, 14-3-3 epsilon binding, and cytoplasmic sequestration of
RT heat shock factor 1.";
RL Mol. Cell. Biol. 23:6013-6026(2003).
RN [21]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC TISSUE=Lymphoblast;
RX PubMed=14654843; DOI=10.1038/nature02166;
RA Andersen J.S., Wilkinson C.J., Mayor T., Mortensen P., Nigg E.A., Mann M.;
RT "Proteomic characterization of the human centrosome by protein correlation
RT profiling.";
RL Nature 426:570-574(2003).
RN [22]
RP INTERACTION WITH GRB10.
RX PubMed=15722337; DOI=10.1074/jbc.m501477200;
RA Urschel S., Bassermann F., Bai R.Y., Munch S., Peschel C., Duyster J.;
RT "Phosphorylation of grb10 regulates its interaction with 14-3-3.";
RL J. Biol. Chem. 280:16987-16993(2005).
RN [23]
RP INTERACTION WITH ABL1, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=15696159; DOI=10.1038/ncb1228;
RA Yoshida K., Yamaguchi T., Natsume T., Kufe D., Miki Y.;
RT "JNK phosphorylation of 14-3-3 proteins regulates nuclear targeting of c-
RT Abl in the apoptotic response to DNA damage.";
RL Nat. Cell Biol. 7:278-285(2005).
RN [24]
RP INTERACTION WITH YWHAZ.
RX PubMed=16376338; DOI=10.1016/j.febslet.2005.12.024;
RA Gu Y.-M., Jin Y.-H., Choi J.-K., Baek K.-H., Yeo C.-Y., Lee K.-Y.;
RT "Protein kinase A phosphorylates and regulates dimerization of 14-3-3
RT epsilon.";
RL FEBS Lett. 580:305-310(2006).
RN [25]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RC TISSUE=Melanoma;
RX PubMed=17081065; DOI=10.1021/pr060363j;
RA Chi A., Valencia J.C., Hu Z.-Z., Watabe H., Yamaguchi H., Mangini N.J.,
RA Huang H., Canfield V.A., Cheng K.C., Yang F., Abe R., Yamagishi S.,
RA Shabanowitz J., Hearing V.J., Wu C., Appella E., Hunt D.F.;
RT "Proteomic and bioinformatic characterization of the biogenesis and
RT function of melanosomes.";
RL J. Proteome Res. 5:3135-3144(2006).
RN [26]
RP INTERACTION WITH ATP2B1 AND ATP2B3.
RX PubMed=18029012; DOI=10.1016/j.ceca.2007.09.003;
RA Linde C.I., Di Leva F., Domi T., Tosatto S.C., Brini M., Carafoli E.;
RT "Inhibitory interaction of the 14-3-3 proteins with ubiquitous (PMCA1) and
RT tissue-specific (PMCA3) isoforms of the plasma membrane Ca2+ pump.";
RL Cell Calcium 43:550-561(2008).
RN [27]
RP INTERACTION WITH GAB2.
RX PubMed=19172738; DOI=10.1038/emboj.2008.159;
RA Brummer T., Larance M., Herrera Abreu M.T., Lyons R.J., Timpson P.,
RA Emmerich C.H., Fleuren E.D.G., Lehrbach G.M., Schramek D., Guilhaus M.,
RA James D.E., Daly R.J.;
RT "Phosphorylation-dependent binding of 14-3-3 terminates signalling by the
RT Gab2 docking protein.";
RL EMBO J. 27:2305-2316(2008).
RN [28]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=18318008; DOI=10.1002/pmic.200700884;
RA Han G., Ye M., Zhou H., Jiang X., Feng S., Jiang X., Tian R., Wan D.,
RA Zou H., Gu J.;
RT "Large-scale phosphoproteome analysis of human liver tissue by enrichment
RT and fractionation of phosphopeptides with strong anion exchange
RT chromatography.";
RL Proteomics 8:1346-1361(2008).
RN [29]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in a
RT refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [30]
RP INTERACTION WITH SLITRK1.
RX PubMed=19640509; DOI=10.1016/j.biopsych.2009.05.033;
RA Kajiwara Y., Buxbaum J.D., Grice D.E.;
RT "SLITRK1 binds 14-3-3 and regulates neurite outgrowth in a phosphorylation-
RT dependent manner.";
RL Biol. Psychiatry 66:918-925(2009).
RN [31]
RP INTERACTION WITH SRPK2.
RX PubMed=19592491; DOI=10.1074/jbc.m109.026237;
RA Jang S.W., Liu X., Fu H., Rees H., Yepes M., Levey A., Ye K.;
RT "Interaction of Akt-phosphorylated SRPK2 with 14-3-3 mediates cell cycle
RT and cell death in neurons.";
RL J. Biol. Chem. 284:24512-24525(2009).
RN [32]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-50; LYS-69; LYS-118 AND LYS-123,
RP AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19608861; DOI=10.1126/science.1175371;
RA Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C.,
RA Olsen J.V., Mann M.;
RT "Lysine acetylation targets protein complexes and co-regulates major
RT cellular functions.";
RL Science 325:834-840(2009).
RN [33]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full phosphorylation
RT site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [34]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [35]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21406692; DOI=10.1126/scisignal.2001570;
RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T.,
RA Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.;
RT "System-wide temporal characterization of the proteome and phosphoproteome
RT of human embryonic stem cell differentiation.";
RL Sci. Signal. 4:RS3-RS3(2011).
RN [36]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Erythroleukemia;
RX PubMed=23186163; DOI=10.1021/pr300630k;
RA Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
RA Mohammed S.;
RT "Toward a comprehensive characterization of a human cancer cell
RT phosphoproteome.";
RL J. Proteome Res. 12:260-271(2013).
RN [37]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-232, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L.,
RA Ye M., Zou H.;
RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver
RT phosphoproteome.";
RL J. Proteomics 96:253-262(2014).
RN [38]
RP INTERACTION WITH DAPK2.
RX PubMed=26047703; DOI=10.1016/j.bbrc.2015.05.105;
RA Yuasa K., Ota R., Matsuda S., Isshiki K., Inoue M., Tsuji A.;
RT "Suppression of death-associated protein kinase 2 by interaction with 14-3-
RT 3 proteins.";
RL Biochem. Biophys. Res. Commun. 464:70-75(2015).
RN [39]
RP INTERACTION WITH DENND1A.
RX PubMed=26055712; DOI=10.1074/jbc.m115.636712;
RA Kulasekaran G., Nossova N., Marat A.L., Lund I., Cremer C., Ioannou M.S.,
RA McPherson P.S.;
RT "Phosphorylation-dependent regulation of Connecdenn/DENND1 guanine
RT nucleotide exchange factors.";
RL J. Biol. Chem. 290:17999-18008(2015).
RN [40]
RP INTERACTION WITH RIPOR2.
RX PubMed=25588844; DOI=10.1242/jcs.161497;
RA Gao K., Tang W., Li Y., Zhang P., Wang D., Yu L., Wang C., Wu D.;
RT "Front-signal-dependent accumulation of the RHOA inhibitor FAM65B at
RT leading edges polarizes neutrophils.";
RL J. Cell Sci. 128:992-1000(2015).
RN [41]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25944712; DOI=10.1002/pmic.201400617;
RA Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D.,
RA Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
RT "N-terminome analysis of the human mitochondrial proteome.";
RL Proteomics 15:2519-2524(2015).
RN [42]
RP INTERACTION WITH MEFV.
RX PubMed=27030597; DOI=10.1126/scitranslmed.aaf1471;
RA Masters S.L., Lagou V., Jeru I., Baker P.J., Van Eyck L., Parry D.A.,
RA Lawless D., De Nardo D., Garcia-Perez J.E., Dagley L.F., Holley C.L.,
RA Dooley J., Moghaddas F., Pasciuto E., Jeandel P.Y., Sciot R., Lyras D.,
RA Webb A.I., Nicholson S.E., De Somer L., van Nieuwenhove E., Ruuth-Praz J.,
RA Copin B., Cochet E., Medlej-Hashim M., Megarbane A., Schroder K., Savic S.,
RA Goris A., Amselem S., Wouters C., Liston A.;
RT "Familial autoinflammation with neutrophilic dermatosis reveals a
RT regulatory mechanism of pyrin activation.";
RL Sci. Transl. Med. 8:332ra45-332ra45(2016).
RN [43]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-50, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=28112733; DOI=10.1038/nsmb.3366;
RA Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
RA Nielsen M.L.;
RT "Site-specific mapping of the human SUMO proteome reveals co-modification
RT with phosphorylation.";
RL Nat. Struct. Mol. Biol. 24:325-336(2017).
RN [44]
RP INTERACTION WITH CRTC1; CRTC2 AND CRTC3.
RX PubMed=30611118; DOI=10.1016/j.isci.2018.12.012;
RA Sonntag T., Ostojic J., Vaughan J.M., Moresco J.J., Yoon Y.S.,
RA Yates J.R. III, Montminy M.;
RT "Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A
RT Recruitment.";
RL IScience 11:134-145(2018).
RN [45]
RP INTERACTION WITH KLHL22.
RX PubMed=29769719; DOI=10.1038/s41586-018-0128-9;
RA Chen J., Ou Y., Yang Y., Li W., Xu Y., Xie Y., Liu Y.;
RT "KLHL22 activates amino-acid-dependent mTORC1 signalling to promote
RT tumorigenesis and ageing.";
RL Nature 557:585-589(2018).
RN [46]
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 1-233, IDENTIFICATION BY MASS
RP SPECTROMETRY, INTERACTION WITH PHOSPHOSERINE MOTIFS, AND SUBUNIT.
RX PubMed=17085597; DOI=10.1073/pnas.0605779103;
RA Yang X., Lee W.H., Sobott F., Papagrigoriou E., Robinson C.V.,
RA Grossmann J.G., Sundstroem M., Doyle D.A., Elkins J.M.;
RT "Structural basis for protein-protein interactions in the 14-3-3 protein
RT family.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:17237-17242(2006).
CC -!- FUNCTION: Adapter protein implicated in the regulation of a large
CC spectrum of both general and specialized signaling pathways. Binds to a
CC large number of partners, usually by recognition of a phosphoserine or
CC phosphothreonine motif. Binding generally results in the modulation of
CC the activity of the binding partner (By similarity). Positively
CC regulates phosphorylated protein HSF1 nuclear export to the cytoplasm
CC (PubMed:12917326). {ECO:0000250|UniProtKB:P62261,
CC ECO:0000269|PubMed:12917326}.
CC -!- SUBUNIT: Homodimer (PubMed:17085597). Heterodimerizes with YWHAZ
CC (PubMed:16376338). Interacts with PKA-phosphorylated AANAT
CC (PubMed:11427721). Interacts with ABL1 (phosphorylated form); the
CC interaction retains it in the cytoplasm (PubMed:15696159). Interacts
CC with ARHGEF28 (By similarity). Interacts with BEX3 (By similarity).
CC Weakly interacts with CDKN1B (PubMed:12042314). Interacts with the
CC 'Thr-369' phosphorylated form of DAPK2 (PubMed:26047703). Interacts
CC with DENND1A (PubMed:26055712). Interacts with GAB2 (PubMed:19172738).
CC Interacts with phosphorylated GRB10 (PubMed:15722337). Interacts with
CC KSR1 (PubMed:10409742). Interacts with NDEL1 (By similarity). Interacts
CC with PI4KB, TBC1D22A and TBC1D22B (PubMed:23572552). Interacts with the
CC phosphorylated (by AKT1) form of SRPK2 (PubMed:19592491). Interacts
CC with TIAM2. Interacts with the 'Ser-1134' and 'Ser-1161' phosphorylated
CC form of SOS1 (By similarity). Interacts with ZFP36 (via phosphorylated
CC form) (By similarity). Interacts with SLITRK1 (PubMed:19640509).
CC Interacts with HSF1 (via phosphorylated form); this interaction
CC promotes HSF1 sequestration in the cytoplasm in a ERK-dependent manner
CC (PubMed:12917326). Interacts with RIPOR2 isoform 2 (PubMed:25588844).
CC Interacts with KLHL22; required for the nuclear localization of KLHL22
CC upon amino acid starvation (PubMed:29769719). Interacts with CRTC1
CC (PubMed:30611118). Interacts with CRTC2 (probably when phosphorylated
CC at 'Ser-171') (PubMed:30611118). Interacts with CRTC3 (probably when
CC phosphorylated at 'Ser-162' and/or 'Ser-273') (PubMed:30611118).
CC Interacts with ATP2B1 and ATP2B3; this interaction inhibits calcium-
CC transporting ATPase activity (PubMed:18029012). Interacts with MEFV
CC (PubMed:27030597). {ECO:0000250|UniProtKB:P62259,
CC ECO:0000250|UniProtKB:P62260, ECO:0000269|PubMed:10409742,
CC ECO:0000269|PubMed:11427721, ECO:0000269|PubMed:12042314,
CC ECO:0000269|PubMed:12917326, ECO:0000269|PubMed:15696159,
CC ECO:0000269|PubMed:15722337, ECO:0000269|PubMed:16376338,
CC ECO:0000269|PubMed:17085597, ECO:0000269|PubMed:18029012,
CC ECO:0000269|PubMed:19172738, ECO:0000269|PubMed:19592491,
CC ECO:0000269|PubMed:19640509, ECO:0000269|PubMed:23572552,
CC ECO:0000269|PubMed:25588844, ECO:0000269|PubMed:26047703,
CC ECO:0000269|PubMed:26055712, ECO:0000269|PubMed:27030597,
CC ECO:0000269|PubMed:29769719, ECO:0000269|PubMed:30611118}.
CC -!- SUBUNIT: (Microbial infection) Interacts with HCV core protein.
CC {ECO:0000269|PubMed:10644344}.
CC -!- INTERACTION:
CC P62258; Q96AP0: ACD; NbExp=2; IntAct=EBI-356498, EBI-717666;
CC P62258; O14727: APAF1; NbExp=2; IntAct=EBI-356498, EBI-446492;
CC P62258; P10398: ARAF; NbExp=4; IntAct=EBI-356498, EBI-365961;
CC P62258; P54253: ATXN1; NbExp=8; IntAct=EBI-356498, EBI-930964;
CC P62258; Q92934: BAD; NbExp=4; IntAct=EBI-356498, EBI-700771;
CC P62258; O00257-3: CBX4; NbExp=2; IntAct=EBI-356498, EBI-4392727;
CC P62258; Q9Y3M2: CBY1; NbExp=3; IntAct=EBI-356498, EBI-947308;
CC P62258; Q86Z20: CCDC125; NbExp=3; IntAct=EBI-356498, EBI-11977221;
CC P62258; O94921: CDK14; NbExp=3; IntAct=EBI-356498, EBI-1043945;
CC P62258; Q9NRI5: DISC1; NbExp=3; IntAct=EBI-356498, EBI-529989;
CC P62258; P09622: DLD; NbExp=5; IntAct=EBI-356498, EBI-353366;
CC P62258; P36957: DLST; NbExp=4; IntAct=EBI-356498, EBI-351007;
CC P62258; Q9UKT5: FBXO4; NbExp=5; IntAct=EBI-356498, EBI-960409;
CC P62258; P56524: HDAC4; NbExp=4; IntAct=EBI-356498, EBI-308629;
CC P62258; P56524-2: HDAC4; NbExp=3; IntAct=EBI-356498, EBI-11953488;
CC P62258; Q14678-2: KANK1; NbExp=3; IntAct=EBI-356498, EBI-6173812;
CC P62258; Q5S007: LRRK2; NbExp=8; IntAct=EBI-356498, EBI-5323863;
CC P62258; Q99759: MAP3K3; NbExp=3; IntAct=EBI-356498, EBI-307281;
CC P62258; O15151: MDM4; NbExp=3; IntAct=EBI-356498, EBI-398437;
CC P62258; P58340: MLF1; NbExp=3; IntAct=EBI-356498, EBI-721328;
CC P62258; Q9NXR1: NDE1; NbExp=2; IntAct=EBI-356498, EBI-941227;
CC P62258; Q7L804: RAB11FIP2; NbExp=3; IntAct=EBI-356498, EBI-1049676;
CC P62258; P04049: RAF1; NbExp=6; IntAct=EBI-356498, EBI-365996;
CC P62258; Q13671: RIN1; NbExp=3; IntAct=EBI-356498, EBI-366017;
CC P62258; Q99469: STAC; NbExp=3; IntAct=EBI-356498, EBI-2652799;
CC P62258; P21796: VDAC1; NbExp=5; IntAct=EBI-356498, EBI-354158;
CC P62258; Q9GZV5: WWTR1; NbExp=3; IntAct=EBI-356498, EBI-747743;
CC P62258; P46937: YAP1; NbExp=5; IntAct=EBI-356498, EBI-1044059;
CC P62258; P31946: YWHAB; NbExp=6; IntAct=EBI-356498, EBI-359815;
CC P62258; P62258: YWHAE; NbExp=3; IntAct=EBI-356498, EBI-356498;
CC P62258; P61981: YWHAG; NbExp=7; IntAct=EBI-356498, EBI-359832;
CC P62258; Q04917: YWHAH; NbExp=5; IntAct=EBI-356498, EBI-306940;
CC P62258; P27348: YWHAQ; NbExp=7; IntAct=EBI-356498, EBI-359854;
CC P62258; P63104: YWHAZ; NbExp=9; IntAct=EBI-356498, EBI-347088;
CC P62258; P61588: Rnd3; Xeno; NbExp=2; IntAct=EBI-356498, EBI-6930266;
CC P62258; PRO_0000278742 [O92972]; Xeno; NbExp=5; IntAct=EBI-356498, EBI-9213553;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12917326}. Cytoplasm
CC {ECO:0000269|PubMed:12917326}. Melanosome {ECO:0000269|PubMed:12042314,
CC ECO:0000269|PubMed:17081065}. Note=Identified by mass spectrometry in
CC melanosome fractions from stage I to stage IV.
CC {ECO:0000269|PubMed:12042314, ECO:0000269|PubMed:17081065}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=P62258-1; Sequence=Displayed;
CC Name=SV;
CC IsoId=P62258-2; Sequence=VSP_040621;
CC -!- MISCELLANEOUS: [Isoform SV]: Unable to dimerize with YWHAZ.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the 14-3-3 family. {ECO:0000305}.
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DR EMBL; U20972; AAC50175.1; -; mRNA.
DR EMBL; U54778; AAC50710.1; -; mRNA.
DR EMBL; U43399; AAC50625.1; -; mRNA.
DR EMBL; U43430; AAD00026.1; -; mRNA.
DR EMBL; U28936; AAA75301.1; -; mRNA.
DR EMBL; AB017103; BAA32538.1; -; Genomic_DNA.
DR EMBL; AY883089; AAX68683.1; -; mRNA.
DR EMBL; AK128785; BAG54733.1; -; mRNA.
DR EMBL; AK295260; BAG58249.1; -; mRNA.
DR EMBL; AK316185; BAH14556.1; -; mRNA.
DR EMBL; BT007161; AAP35825.1; -; mRNA.
DR EMBL; CH471108; EAW90628.1; -; Genomic_DNA.
DR EMBL; CH471108; EAW90629.1; -; Genomic_DNA.
DR EMBL; BC000179; AAH00179.1; -; mRNA.
DR EMBL; BC001440; AAH01440.1; -; mRNA.
DR CCDS; CCDS11001.1; -. [P62258-1]
DR PIR; A61235; A61235.
DR PIR; I38947; I38947.
DR RefSeq; NP_006752.1; NM_006761.4. [P62258-1]
DR PDB; 2BR9; X-ray; 1.75 A; A=1-233.
DR PDB; 3UAL; X-ray; 1.80 A; A=1-232.
DR PDB; 3UBW; X-ray; 1.90 A; A=1-234.
DR PDB; 6EIH; X-ray; 2.70 A; A=3-232.
DR PDB; 7C8E; X-ray; 3.16 A; A/B=1-232.
DR PDBsum; 2BR9; -.
DR PDBsum; 3UAL; -.
DR PDBsum; 3UBW; -.
DR PDBsum; 6EIH; -.
DR PDBsum; 7C8E; -.
DR AlphaFoldDB; P62258; -.
DR SMR; P62258; -.
DR BioGRID; 113363; 939.
DR CORUM; P62258; -.
DR DIP; DIP-36676N; -.
DR ELM; P62258; -.
DR IntAct; P62258; 290.
DR MINT; P62258; -.
DR STRING; 9606.ENSP00000264335; -.
DR ChEMBL; CHEMBL3329082; -.
DR DrugBank; DB01780; Fusicoccin.
DR DrugBank; DB12695; Phenethyl Isothiocyanate.
DR MoonDB; P62258; Predicted.
DR GlyGen; P62258; 1 site, 1 O-linked glycan (1 site).
DR iPTMnet; P62258; -.
DR MetOSite; P62258; -.
DR PhosphoSitePlus; P62258; -.
DR SwissPalm; P62258; -.
DR BioMuta; YWHAE; -.
DR DMDM; 51702210; -.
DR OGP; P42655; -.
DR UCD-2DPAGE; P62258; -.
DR EPD; P62258; -.
DR jPOST; P62258; -.
DR MassIVE; P62258; -.
DR MaxQB; P62258; -.
DR PaxDb; P62258; -.
DR PeptideAtlas; P62258; -.
DR PRIDE; P62258; -.
DR ProteomicsDB; 57377; -.
DR ProteomicsDB; 57378; -. [P62258-2]
DR TopDownProteomics; P62258-1; -. [P62258-1]
DR Antibodypedia; 1898; 503 antibodies from 39 providers.
DR CPTC; P62258; 3 antibodies.
DR DNASU; 7531; -.
DR Ensembl; ENST00000264335.13; ENSP00000264335.8; ENSG00000108953.17. [P62258-1]
DR Ensembl; ENST00000571732.5; ENSP00000461762.1; ENSG00000108953.17. [P62258-2]
DR Ensembl; ENST00000616643.3; ENSP00000481059.2; ENSG00000274474.3. [P62258-2]
DR Ensembl; ENST00000627231.2; ENSP00000487356.1; ENSG00000274474.3. [P62258-1]
DR GeneID; 7531; -.
DR KEGG; hsa:7531; -.
DR MANE-Select; ENST00000264335.13; ENSP00000264335.8; NM_006761.5; NP_006752.1.
DR UCSC; uc002fsk.4; human. [P62258-1]
DR CTD; 7531; -.
DR DisGeNET; 7531; -.
DR GeneCards; YWHAE; -.
DR HGNC; HGNC:12851; YWHAE.
DR HPA; ENSG00000108953; Low tissue specificity.
DR MalaCards; YWHAE; -.
DR MIM; 605066; gene.
DR neXtProt; NX_P62258; -.
DR OpenTargets; ENSG00000108953; -.
DR Orphanet; 217385; 17p13.3 microduplication syndrome.
DR Orphanet; 457246; Clear cell sarcoma of kidney.
DR Orphanet; 261257; Distal 17p13.3 microdeletion syndrome.
DR Orphanet; 213711; Endometrial stromal sarcoma.
DR Orphanet; 531; Miller-Dieker syndrome.
DR PharmGKB; PA37440; -.
DR VEuPathDB; HostDB:ENSG00000108953; -.
DR eggNOG; KOG0841; Eukaryota.
DR GeneTree; ENSGT01050000244964; -.
DR HOGENOM; CLU_058290_0_0_1; -.
DR InParanoid; P62258; -.
DR OMA; IPCATTG; -.
DR PhylomeDB; P62258; -.
DR TreeFam; TF102003; -.
DR PathwayCommons; P62258; -.
DR Reactome; R-HSA-111447; Activation of BAD and translocation to mitochondria.
DR Reactome; R-HSA-1445148; Translocation of SLC2A4 (GLUT4) to the plasma membrane.
DR Reactome; R-HSA-2028269; Signaling by Hippo.
DR Reactome; R-HSA-205025; NADE modulates death signalling.
DR Reactome; R-HSA-2565942; Regulation of PLK1 Activity at G2/M Transition.
DR Reactome; R-HSA-3371453; Regulation of HSF1-mediated heat shock response.
DR Reactome; R-HSA-3371511; HSF1 activation.
DR Reactome; R-HSA-380259; Loss of Nlp from mitotic centrosomes.
DR Reactome; R-HSA-380270; Recruitment of mitotic centrosome proteins and complexes.
DR Reactome; R-HSA-380284; Loss of proteins required for interphase microtubule organization from the centrosome.
DR Reactome; R-HSA-380320; Recruitment of NuMA to mitotic centrosomes.
DR Reactome; R-HSA-5620912; Anchoring of the basal body to the plasma membrane.
DR Reactome; R-HSA-5625740; RHO GTPases activate PKNs.
DR Reactome; R-HSA-5628897; TP53 Regulates Metabolic Genes.
DR Reactome; R-HSA-75035; Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex.
DR Reactome; R-HSA-8854518; AURKA Activation by TPX2.
DR Reactome; R-HSA-8862803; Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models.
DR Reactome; R-HSA-8876198; RAB GEFs exchange GTP for GDP on RABs.
DR Reactome; R-HSA-9755779; SARS-CoV-2 targets host intracellular signalling and regulatory pathways.
DR SignaLink; P62258; -.
DR SIGNOR; P62258; -.
DR BioGRID-ORCS; 7531; 201 hits in 1049 CRISPR screens.
DR ChiTaRS; YWHAE; human.
DR EvolutionaryTrace; P62258; -.
DR GeneWiki; YWHAE; -.
DR GenomeRNAi; 7531; -.
DR Pharos; P62258; Tbio.
DR PRO; PR:P62258; -.
DR Proteomes; UP000005640; Chromosome 17.
DR RNAct; P62258; protein.
DR Bgee; ENSG00000108953; Expressed in superior frontal gyrus and 114 other tissues.
DR ExpressionAtlas; P62258; baseline and differential.
DR Genevisible; P62258; HS.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IDA:HPA.
DR GO; GO:0070062; C:extracellular exosome; HDA:UniProtKB.
DR GO; GO:0005925; C:focal adhesion; HDA:UniProtKB.
DR GO; GO:0042470; C:melanosome; IEA:UniProtKB-SubCell.
DR GO; GO:0016020; C:membrane; HDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0045296; F:cadherin binding; HDA:BHF-UCL.
DR GO; GO:0005246; F:calcium channel regulator activity; IDA:SynGO-UCL.
DR GO; GO:0019899; F:enzyme binding; IPI:UniProtKB.
DR GO; GO:0042826; F:histone deacetylase binding; IPI:BHF-UCL.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0023026; F:MHC class II protein complex binding; HDA:UniProtKB.
DR GO; GO:0051219; F:phosphoprotein binding; IPI:BHF-UCL.
DR GO; GO:0050815; F:phosphoserine residue binding; IPI:BHF-UCL.
DR GO; GO:0015459; F:potassium channel regulator activity; IDA:BHF-UCL.
DR GO; GO:0019904; F:protein domain specific binding; IEA:Ensembl.
DR GO; GO:0046982; F:protein heterodimerization activity; IPI:BHF-UCL.
DR GO; GO:0019903; F:protein phosphatase binding; IEA:Ensembl.
DR GO; GO:0003723; F:RNA binding; HDA:UniProtKB.
DR GO; GO:0097110; F:scaffold protein binding; IPI:UniProtKB.
DR GO; GO:0044325; F:transmembrane transporter binding; IPI:BHF-UCL.
DR GO; GO:0031625; F:ubiquitin protein ligase binding; IPI:ParkinsonsUK-UCL.
DR GO; GO:0034605; P:cellular response to heat; IDA:UniProtKB.
DR GO; GO:0021987; P:cerebral cortex development; IEA:Ensembl.
DR GO; GO:0021766; P:hippocampus development; IEA:Ensembl.
DR GO; GO:0035556; P:intracellular signal transduction; TAS:ProtInc.
DR GO; GO:0000165; P:MAPK cascade; IDA:UniProtKB.
DR GO; GO:0086013; P:membrane repolarization during cardiac muscle cell action potential; IC:BHF-UCL.
DR GO; GO:1905913; P:negative regulation of calcium ion export across plasma membrane; IDA:SynGO-UCL.
DR GO; GO:1901020; P:negative regulation of calcium ion transmembrane transporter activity; IDA:SynGO-UCL.
DR GO; GO:1902309; P:negative regulation of peptidyl-serine dephosphorylation; IDA:BHF-UCL.
DR GO; GO:0001764; P:neuron migration; IEA:Ensembl.
DR GO; GO:0046827; P:positive regulation of protein export from nucleus; IDA:UniProtKB.
DR GO; GO:0008104; P:protein localization; IBA:GO_Central.
DR GO; GO:0034504; P:protein localization to nucleus; IMP:UniProtKB.
DR GO; GO:0006605; P:protein targeting; IEA:Ensembl.
DR GO; GO:0051480; P:regulation of cytosolic calcium ion concentration; IDA:SynGO-UCL.
DR GO; GO:0086091; P:regulation of heart rate by cardiac conduction; IC:BHF-UCL.
DR GO; GO:0003064; P:regulation of heart rate by hormone; NAS:BHF-UCL.
DR GO; GO:0060306; P:regulation of membrane repolarization; IDA:BHF-UCL.
DR GO; GO:0007346; P:regulation of mitotic cell cycle; IBA:GO_Central.
DR GO; GO:1901016; P:regulation of potassium ion transmembrane transporter activity; IDA:BHF-UCL.
DR GO; GO:0007165; P:signal transduction; IBA:GO_Central.
DR GO; GO:0021762; P:substantia nigra development; HEP:UniProtKB.
DR Gene3D; 1.20.190.20; -; 1.
DR IDEAL; IID00512; -.
DR InterPro; IPR000308; 14-3-3.
DR InterPro; IPR023409; 14-3-3_CS.
DR InterPro; IPR036815; 14-3-3_dom_sf.
DR InterPro; IPR023410; 14-3-3_domain.
DR PANTHER; PTHR18860; PTHR18860; 1.
DR Pfam; PF00244; 14-3-3; 1.
DR PIRSF; PIRSF000868; 14-3-3; 1.
DR PRINTS; PR00305; 1433ZETA.
DR SMART; SM00101; 14_3_3; 1.
DR SUPFAM; SSF48445; SSF48445; 1.
DR PROSITE; PS00796; 1433_1; 1.
DR PROSITE; PS00797; 1433_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative splicing; Cytoplasm;
KW Direct protein sequencing; Host-virus interaction; Isopeptide bond;
KW Nucleus; Phosphoprotein; Reference proteome; Ubl conjugation.
FT CHAIN 1..255
FT /note="14-3-3 protein epsilon"
FT /id="PRO_0000058618"
FT REGION 234..255
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 238..255
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 57
FT /note="Interaction with phosphoserine on interacting
FT protein"
FT SITE 130
FT /note="Interaction with phosphoserine on interacting
FT protein"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000269|Ref.13, ECO:0007744|PubMed:19413330"
FT MOD_RES 50
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0007744|PubMed:19608861"
FT MOD_RES 65
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P62260"
FT MOD_RES 69
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:19608861"
FT MOD_RES 118
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:19608861"
FT MOD_RES 123
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:19608861"
FT MOD_RES 131
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000250|UniProtKB:P62260"
FT MOD_RES 137
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:P62260"
FT MOD_RES 210
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:20068231,
FT ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163"
FT MOD_RES 232
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:24275569"
FT CROSSLNK 50
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2); alternate"
FT /evidence="ECO:0007744|PubMed:28112733"
FT VAR_SEQ 1..22
FT /note="Missing (in isoform SV)"
FT /evidence="ECO:0000303|PubMed:14702039,
FT ECO:0000303|PubMed:20417184"
FT /id="VSP_040621"
FT CONFLICT 106..107
FT /note="KH -> NY (in Ref. 15; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 143
FT /note="E -> F (in Ref. 15; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 148
FT /note="S -> T (in Ref. 15; AA sequence)"
FT /evidence="ECO:0000305"
FT HELIX 4..17
FT /evidence="ECO:0007829|PDB:2BR9"
FT HELIX 20..31
FT /evidence="ECO:0007829|PDB:2BR9"
FT HELIX 39..73
FT /evidence="ECO:0007829|PDB:2BR9"
FT HELIX 76..106
FT /evidence="ECO:0007829|PDB:2BR9"
FT HELIX 108..111
FT /evidence="ECO:0007829|PDB:2BR9"
FT HELIX 115..135
FT /evidence="ECO:0007829|PDB:2BR9"
FT HELIX 138..162
FT /evidence="ECO:0007829|PDB:2BR9"
FT HELIX 168..183
FT /evidence="ECO:0007829|PDB:2BR9"
FT HELIX 188..204
FT /evidence="ECO:0007829|PDB:2BR9"
FT HELIX 205..208
FT /evidence="ECO:0007829|PDB:2BR9"
FT TURN 211..213
FT /evidence="ECO:0007829|PDB:2BR9"
FT HELIX 214..231
FT /evidence="ECO:0007829|PDB:2BR9"
SQ SEQUENCE 255 AA; 29174 MW; 07817CCBD1F75B26 CRC64;
MDDREDLVYQ AKLAEQAERY DEMVESMKKV AGMDVELTVE ERNLLSVAYK NVIGARRASW
RIISSIEQKE ENKGGEDKLK MIREYRQMVE TELKLICCDI LDVLDKHLIP AANTGESKVF
YYKMKGDYHR YLAEFATGND RKEAAENSLV AYKAASDIAM TELPPTHPIR LGLALNFSVF
YYEILNSPDR ACRLAKAAFD DAIAELDTLS EESYKDSTLI MQLLRDNLTL WTSDMQGDGE
EQNKEALQDV EDENQ
//

83
Tests/SwissProt/P68308.txt Normal file
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@ -0,0 +1,83 @@
ID NU3M_BALPH Reviewed; 115 AA.
AC P68308; P24973;
DT 25-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2004, sequence version 1.
DT 25-MAY-2022, entry version 57.
DE RecName: Full=NADH-ubiquinone oxidoreductase chain 3 {ECO:0000250|UniProtKB:P03897};
DE EC=7.1.1.2 {ECO:0000250|UniProtKB:P03897};
DE AltName: Full=NADH dehydrogenase subunit 3;
GN Name=MT-ND3 {ECO:0000250|UniProtKB:P03897};
GN Synonyms=MTND3, NADH3, ND3;
OS Balaenoptera physalus (Fin whale) (Balaena physalus).
OG Mitochondrion.
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea; Mysticeti;
OC Balaenopteridae; Balaenoptera.
OX NCBI_TaxID=9770;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=Isolate No. 27 / Anno 1987; TISSUE=Liver;
RX PubMed=1779436; DOI=10.1007/bf02102808;
RA Arnason U., Gullberg A., Widegren B.;
RT "The complete nucleotide sequence of the mitochondrial DNA of the fin
RT whale, Balaenoptera physalus.";
RL J. Mol. Evol. 33:556-568(1991).
CC -!- FUNCTION: Core subunit of the mitochondrial membrane respiratory chain
CC NADH dehydrogenase (Complex I) which catalyzes electron transfer from
CC NADH through the respiratory chain, using ubiquinone as an electron
CC acceptor. Essential for the catalytic activity of complex I.
CC {ECO:0000250|UniProtKB:P03897}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) +
CC NAD(+); Xref=Rhea:RHEA:29091, Rhea:RHEA-COMP:9565, Rhea:RHEA-
CC COMP:9566, ChEBI:CHEBI:15378, ChEBI:CHEBI:16389, ChEBI:CHEBI:17976,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=7.1.1.2;
CC Evidence={ECO:0000250|UniProtKB:P03897};
CC -!- SUBUNIT: Core subunit of respiratory chain NADH dehydrogenase (Complex
CC I) which is composed of 45 different subunits. Interacts with TMEM186.
CC Interacts with TMEM242 (By similarity). {ECO:0000250|UniProtKB:P03897}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion inner membrane
CC {ECO:0000250|UniProtKB:P03898}; Multi-pass membrane protein
CC {ECO:0000255}.
CC -!- SIMILARITY: Belongs to the complex I subunit 3 family. {ECO:0000305}.
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DR EMBL; X61145; CAA43446.1; -; Genomic_DNA.
DR PIR; H58850; H58850.
DR RefSeq; NP_006896.1; NC_001321.1.
DR AlphaFoldDB; P68308; -.
DR SMR; P68308; -.
DR GeneID; 807610; -.
DR CTD; 4537; -.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005743; C:mitochondrial inner membrane; ISS:UniProtKB.
DR GO; GO:0070469; C:respirasome; IEA:UniProtKB-KW.
DR GO; GO:0008137; F:NADH dehydrogenase (ubiquinone) activity; ISS:UniProtKB.
DR GO; GO:0006120; P:mitochondrial electron transport, NADH to ubiquinone; ISS:UniProtKB.
DR Gene3D; 1.20.58.1610; -; 1.
DR InterPro; IPR000440; NADH_UbQ/plastoQ_OxRdtase_su3.
DR InterPro; IPR038430; NDAH_ubi_oxred_su3_sf.
DR PANTHER; PTHR11058; PTHR11058; 1.
DR Pfam; PF00507; Oxidored_q4; 1.
PE 3: Inferred from homology;
KW Electron transport; Membrane; Mitochondrion; Mitochondrion inner membrane;
KW NAD; Respiratory chain; Translocase; Transmembrane; Transmembrane helix;
KW Transport; Ubiquinone.
FT CHAIN 1..115
FT /note="NADH-ubiquinone oxidoreductase chain 3"
FT /id="PRO_0000117714"
FT TRANSMEM 3..23
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 55..75
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 84..104
FT /note="Helical"
FT /evidence="ECO:0000255"
SQ SEQUENCE 115 AA; 13022 MW; 405197D2F5D0AC4B CRC64;
MNLLLTLLTN TTLALLLVFI AFWLPQLNVY AEKTSPYECG FDPMGSARLP FSMKFFLVAI
TFLLFDLEIA LLLPLPWAIQ SNNLNTMLTM ALFLISLLAA SLAYEWTQEG LEWAE
//

396
Tests/SwissProt/Q13454.txt Normal file
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@ -0,0 +1,396 @@
ID TUSC3_HUMAN Reviewed; 348 AA.
AC Q13454; A8MSM0; D3DSP2; Q14911; Q14912; Q96FW0;
DT 15-JUL-1999, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 12-OCT-2022, entry version 184.
DE RecName: Full=Tumor suppressor candidate 3;
DE AltName: Full=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TUSC3;
DE Short=Oligosaccharyl transferase subunit TUSC3;
DE AltName: Full=Magnesium uptake/transporter TUSC3;
DE AltName: Full=Protein N33;
DE Flags: Precursor;
GN Name=TUSC3; Synonyms=N33;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORMS 1 AND 2).
RX PubMed=8661104; DOI=10.1006/geno.1996.0322;
RA Macgrogan D., Levy A., Bova G.S., Isaacs W.B., Bookstein R.;
RT "Structure and methylation-associated silencing of a gene within a
RT homozygously deleted region of human chromosome band 8p22.";
RL Genomics 35:55-65(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S.,
RA Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y.,
RA Phelan M., Farmer A.;
RT "Cloning of human full-length CDSs in BD Creator(TM) system donor vector.";
RL Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16421571; DOI=10.1038/nature04406;
RA Nusbaum C., Mikkelsen T.S., Zody M.C., Asakawa S., Taudien S., Garber M.,
RA Kodira C.D., Schueler M.G., Shimizu A., Whittaker C.A., Chang J.L.,
RA Cuomo C.A., Dewar K., FitzGerald M.G., Yang X., Allen N.R., Anderson S.,
RA Asakawa T., Blechschmidt K., Bloom T., Borowsky M.L., Butler J., Cook A.,
RA Corum B., DeArellano K., DeCaprio D., Dooley K.T., Dorris L. III,
RA Engels R., Gloeckner G., Hafez N., Hagopian D.S., Hall J.L., Ishikawa S.K.,
RA Jaffe D.B., Kamat A., Kudoh J., Lehmann R., Lokitsang T., Macdonald P.,
RA Major J.E., Matthews C.D., Mauceli E., Menzel U., Mihalev A.H.,
RA Minoshima S., Murayama Y., Naylor J.W., Nicol R., Nguyen C., O'Leary S.B.,
RA O'Neill K., Parker S.C.J., Polley A., Raymond C.K., Reichwald K.,
RA Rodriguez J., Sasaki T., Schilhabel M., Siddiqui R., Smith C.L.,
RA Sneddon T.P., Talamas J.A., Tenzin P., Topham K., Venkataraman V., Wen G.,
RA Yamazaki S., Young S.K., Zeng Q., Zimmer A.R., Rosenthal A., Birren B.W.,
RA Platzer M., Shimizu N., Lander E.S.;
RT "DNA sequence and analysis of human chromosome 8.";
RL Nature 439:331-335(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Skin;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [6]
RP IDENTIFICATION IN THE OLIGOSACCHARYLTRANSFERASE (OST) COMPLEX, AND TISSUE
RP SPECIFICITY.
RX PubMed=12887896; DOI=10.1016/s1097-2765(03)00243-0;
RA Kelleher D.J., Karaoglu D., Mandon E.C., Gilmore R.;
RT "Oligosaccharyltransferase isoforms that contain different catalytic STT3
RT subunits have distinct enzymatic properties.";
RL Mol. Cell 12:101-111(2003).
RN [7]
RP INVOLVEMENT IN MRT7.
RX PubMed=18455129; DOI=10.1016/j.ajhg.2008.03.021;
RA Molinari F., Foulquier F., Tarpey P.S., Morelle W., Boissel S., Teague J.,
RA Edkins S., Futreal P.A., Stratton M.R., Turner G., Matthijs G., Gecz J.,
RA Munnich A., Colleaux L.;
RT "Oligosaccharyltransferase-subunit mutations in nonsyndromic mental
RT retardation.";
RL Am. J. Hum. Genet. 82:1150-1157(2008).
RN [8]
RP INVOLVEMENT IN MRT7.
RX PubMed=18452889; DOI=10.1016/j.ajhg.2008.03.018;
RA Garshasbi M., Hadavi V., Habibi H., Kahrizi K., Kariminejad R., Behjati F.,
RA Tzschach A., Najmabadi H., Ropers H.H., Kuss A.W.;
RT "A defect in the TUSC3 gene is associated with autosomal recessive mental
RT retardation.";
RL Am. J. Hum. Genet. 82:1158-1164(2008).
RN [9]
RP FUNCTION IN MAGNESIUM UPTAKE.
RX PubMed=19717468; DOI=10.1073/pnas.0908332106;
RA Zhou H., Clapham D.E.;
RT "Mammalian MagT1 and TUSC3 are required for cellular magnesium uptake and
RT vertebrate embryonic development.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:15750-15755(2009).
RN [10]
RP FUNCTION, AND MUTAGENESIS OF CYS-99 AND CYS-102.
RX PubMed=25135935; DOI=10.1083/jcb.201404083;
RA Cherepanova N.A., Shrimal S., Gilmore R.;
RT "Oxidoreductase activity is necessary for N-glycosylation of cysteine-
RT proximal acceptor sites in glycoproteins.";
RL J. Cell Biol. 206:525-539(2014).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.10 ANGSTROMS) OF 44-194, DISULFIDE BOND, PROPOSED
RP FUNCTION, AND SUBUNIT.
RX PubMed=24685145; DOI=10.1016/j.str.2014.02.013;
RA Mohorko E., Owen R.L., Malojcic G., Brozzo M.S., Aebi M., Glockshuber R.;
RT "Structural basis of substrate specificity of human oligosaccharyl
RT transferase subunit N33/Tusc3 and its role in regulating protein N-
RT glycosylation.";
RL Structure 22:590-601(2014).
RN [12]
RP VARIANT VAL-247.
RX PubMed=23033978; DOI=10.1056/nejmoa1206524;
RA de Ligt J., Willemsen M.H., van Bon B.W., Kleefstra T., Yntema H.G.,
RA Kroes T., Vulto-van Silfhout A.T., Koolen D.A., de Vries P., Gilissen C.,
RA del Rosario M., Hoischen A., Scheffer H., de Vries B.B., Brunner H.G.,
RA Veltman J.A., Vissers L.E.;
RT "Diagnostic exome sequencing in persons with severe intellectual
RT disability.";
RL N. Engl. J. Med. 367:1921-1929(2012).
CC -!- FUNCTION: Acts as accessory component of the N-oligosaccharyl
CC transferase (OST) complex which catalyzes the transfer of a high
CC mannose oligosaccharide from a lipid-linked oligosaccharide donor to an
CC asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent
CC polypeptide chains. Involved in N-glycosylation of STT3B-dependent
CC substrates. Specifically required for the glycosylation of a subset of
CC acceptor sites that are near cysteine residues; in this function seems
CC to act redundantly with MAGT1. In its oxidized form proposed to form
CC transient mixed disulfides with a glycoprotein substrate to facilitate
CC access of STT3B to the unmodified acceptor site. Has also
CC oxidoreductase-independent functions in the STT3B-containing OST
CC complex possibly involving substrate recognition.
CC {ECO:0000269|PubMed:25135935, ECO:0000305|PubMed:12887896,
CC ECO:0000305|PubMed:24685145}.
CC -!- FUNCTION: Magnesium transporter. {ECO:0000269|PubMed:19717468}.
CC -!- PATHWAY: Protein modification; protein glycosylation.
CC -!- SUBUNIT: Accessory component of the STT3B-containing form of the
CC oligosaccharyltransferase (OST) complex. OST exists in two different
CC complex forms which contain common core subunits RPN1, RPN2, OST48,
CC OST4, DAD1 and TMEM258, either STT3A or STT3B as catalytic subunits,
CC and form-specific accessory subunits. OST can form stable complexes
CC with the Sec61 complex or with both the Sec61 and TRAP complexes. The
CC association of TUSC3 or MAGT1 with the STT3B-containing complex seems
CC to be mutually exclusvice. {ECO:0000305|PubMed:12887896,
CC ECO:0000305|PubMed:24685145}.
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane {ECO:0000250};
CC Multi-pass membrane protein {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q13454-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q13454-2; Sequence=VSP_003776;
CC -!- TISSUE SPECIFICITY: Expressed in most non-lymphoid cells and tissues
CC examined, including prostate, lung, liver, colon, heart, kidney and
CC pancreas. {ECO:0000269|PubMed:12887896}.
CC -!- DISEASE: Intellectual developmental disorder, autosomal recessive 7
CC (MRT7) [MIM:611093]: A disorder characterized by significantly below
CC average general intellectual functioning associated with impairments in
CC adaptive behavior and manifested during the developmental period.
CC {ECO:0000269|PubMed:18452889, ECO:0000269|PubMed:18455129}. Note=The
CC disease is caused by variants affecting the gene represented in this
CC entry.
CC -!- SIMILARITY: Belongs to the OST3/OST6 family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U42349; AAB18374.1; -; mRNA.
DR EMBL; U42359; AAB18375.1; -; Genomic_DNA.
DR EMBL; U42350; AAB18375.1; JOINED; Genomic_DNA.
DR EMBL; U42351; AAB18375.1; JOINED; Genomic_DNA.
DR EMBL; U42352; AAB18375.1; JOINED; Genomic_DNA.
DR EMBL; U42354; AAB18375.1; JOINED; Genomic_DNA.
DR EMBL; U42355; AAB18375.1; JOINED; Genomic_DNA.
DR EMBL; U42356; AAB18375.1; JOINED; Genomic_DNA.
DR EMBL; U42357; AAB18375.1; JOINED; Genomic_DNA.
DR EMBL; U42358; AAB18375.1; JOINED; Genomic_DNA.
DR EMBL; U42360; AAB18376.1; -; Genomic_DNA.
DR EMBL; U42350; AAB18376.1; JOINED; Genomic_DNA.
DR EMBL; U42351; AAB18376.1; JOINED; Genomic_DNA.
DR EMBL; U42352; AAB18376.1; JOINED; Genomic_DNA.
DR EMBL; U42354; AAB18376.1; JOINED; Genomic_DNA.
DR EMBL; U42355; AAB18376.1; JOINED; Genomic_DNA.
DR EMBL; U42356; AAB18376.1; JOINED; Genomic_DNA.
DR EMBL; U42357; AAB18376.1; JOINED; Genomic_DNA.
DR EMBL; U42358; AAB18376.1; JOINED; Genomic_DNA.
DR EMBL; BT020002; AAV38805.1; -; mRNA.
DR EMBL; AC010656; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AC019292; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AC091559; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AC100850; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471080; EAW63837.1; -; Genomic_DNA.
DR EMBL; CH471080; EAW63839.1; -; Genomic_DNA.
DR EMBL; BC010370; AAH10370.1; -; mRNA.
DR CCDS; CCDS5993.1; -. [Q13454-2]
DR CCDS; CCDS5994.1; -. [Q13454-1]
DR PIR; G02297; G02297.
DR RefSeq; NP_006756.2; NM_006765.3. [Q13454-1]
DR RefSeq; NP_839952.1; NM_178234.2. [Q13454-2]
DR PDB; 4M8G; X-ray; 2.00 A; A/B=44-194.
DR PDB; 4M90; X-ray; 1.60 A; A=44-194.
DR PDB; 4M91; X-ray; 1.10 A; A=44-194.
DR PDB; 4M92; X-ray; 1.60 A; A=44-194.
DR PDBsum; 4M8G; -.
DR PDBsum; 4M90; -.
DR PDBsum; 4M91; -.
DR PDBsum; 4M92; -.
DR AlphaFoldDB; Q13454; -.
DR SMR; Q13454; -.
DR BioGRID; 113701; 64.
DR CORUM; Q13454; -.
DR IntAct; Q13454; 21.
DR MINT; Q13454; -.
DR STRING; 9606.ENSP00000424544; -.
DR TCDB; 1.A.76.1.2; the magnesium transporter1 (magt1) family.
DR TCDB; 9.B.142.3.17; the integral membrane glycosyltransferase family 39 (gt39) family.
DR iPTMnet; Q13454; -.
DR PhosphoSitePlus; Q13454; -.
DR BioMuta; TUSC3; -.
DR DMDM; 6166601; -.
DR EPD; Q13454; -.
DR jPOST; Q13454; -.
DR MassIVE; Q13454; -.
DR MaxQB; Q13454; -.
DR PaxDb; Q13454; -.
DR PeptideAtlas; Q13454; -.
DR PRIDE; Q13454; -.
DR ProteomicsDB; 59456; -. [Q13454-1]
DR ProteomicsDB; 59457; -. [Q13454-2]
DR Antibodypedia; 22197; 183 antibodies from 28 providers.
DR DNASU; 7991; -.
DR Ensembl; ENST00000382020.8; ENSP00000371450.4; ENSG00000104723.21. [Q13454-2]
DR Ensembl; ENST00000503731.6; ENSP00000424544.1; ENSG00000104723.21. [Q13454-1]
DR GeneID; 7991; -.
DR KEGG; hsa:7991; -.
DR MANE-Select; ENST00000503731.6; ENSP00000424544.1; NM_006765.4; NP_006756.2.
DR UCSC; uc003wwt.4; human. [Q13454-1]
DR CTD; 7991; -.
DR DisGeNET; 7991; -.
DR GeneCards; TUSC3; -.
DR GeneReviews; TUSC3; -.
DR HGNC; HGNC:30242; TUSC3.
DR HPA; ENSG00000104723; Low tissue specificity.
DR MalaCards; TUSC3; -.
DR MIM; 601385; gene.
DR MIM; 611093; phenotype.
DR neXtProt; NX_Q13454; -.
DR OpenTargets; ENSG00000104723; -.
DR Orphanet; 88616; Autosomal recessive non-syndromic intellectual disability.
DR PharmGKB; PA128394537; -.
DR VEuPathDB; HostDB:ENSG00000104723; -.
DR eggNOG; KOG2603; Eukaryota.
DR GeneTree; ENSGT00390000012030; -.
DR InParanoid; Q13454; -.
DR OMA; NLWAAVS; -.
DR OrthoDB; 1460433at2759; -.
DR PhylomeDB; Q13454; -.
DR TreeFam; TF314850; -.
DR PathwayCommons; Q13454; -.
DR Reactome; R-HSA-446203; Asparagine N-linked glycosylation.
DR Reactome; R-HSA-5223345; Miscellaneous transport and binding events.
DR Reactome; R-HSA-9694548; Maturation of spike protein.
DR SignaLink; Q13454; -.
DR UniPathway; UPA00378; -.
DR BioGRID-ORCS; 7991; 106 hits in 1077 CRISPR screens.
DR ChiTaRS; TUSC3; human.
DR GeneWiki; TUSC3; -.
DR GenomeRNAi; 7991; -.
DR Pharos; Q13454; Tbio.
DR PRO; PR:Q13454; -.
DR Proteomes; UP000005640; Chromosome 8.
DR RNAct; Q13454; protein.
DR Bgee; ENSG00000104723; Expressed in type B pancreatic cell and 185 other tissues.
DR ExpressionAtlas; Q13454; baseline and differential.
DR Genevisible; Q13454; HS.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; TAS:Reactome.
DR GO; GO:0005887; C:integral component of plasma membrane; NAS:UniProtKB.
DR GO; GO:0005739; C:mitochondrion; ISS:UniProtKB.
DR GO; GO:0008250; C:oligosaccharyltransferase complex; IDA:HGNC-UCL.
DR GO; GO:0005886; C:plasma membrane; TAS:Reactome.
DR GO; GO:0015095; F:magnesium ion transmembrane transporter activity; IMP:UniProtKB.
DR GO; GO:0050890; P:cognition; IMP:UniProtKB.
DR GO; GO:0015693; P:magnesium ion transport; IMP:UniProtKB.
DR GO; GO:0006487; P:protein N-linked glycosylation; NAS:UniProtKB.
DR GO; GO:0018279; P:protein N-linked glycosylation via asparagine; IMP:UniProtKB.
DR GO; GO:0055085; P:transmembrane transport; TAS:Reactome.
DR InterPro; IPR021149; OligosaccharylTrfase_OST3/OST6.
DR InterPro; IPR036249; Thioredoxin-like_sf.
DR PANTHER; PTHR12692; PTHR12692; 1.
DR Pfam; PF04756; OST3_OST6; 1.
DR SUPFAM; SSF52833; SSF52833; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Disulfide bond; Endoplasmic reticulum;
KW Intellectual disability; Magnesium; Membrane; Reference proteome; Signal;
KW Transmembrane; Transmembrane helix; Transport.
FT SIGNAL 1..41
FT /evidence="ECO:0000255"
FT CHAIN 42..348
FT /note="Tumor suppressor candidate 3"
FT /id="PRO_0000215300"
FT TOPO_DOM 42..196
FT /note="Lumenal"
FT /evidence="ECO:0000255"
FT TRANSMEM 197..217
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 218..221
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 222..242
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 243..276
FT /note="Lumenal"
FT /evidence="ECO:0000255"
FT TRANSMEM 277..297
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 298..312
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 313..333
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 334..348
FT /note="Lumenal"
FT /evidence="ECO:0000255"
FT DOMAIN 59..187
FT /note="Thioredoxin"
FT DISULFID 99..102
FT /note="Redox-active"
FT /evidence="ECO:0000269|PubMed:24685145,
FT ECO:0007744|PDB:4M8G, ECO:0007744|PDB:4M90"
FT VAR_SEQ 344..348
FT /note="DLDFE -> FLIK (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334,
FT ECO:0000303|PubMed:8661104"
FT /id="VSP_003776"
FT VARIANT 65
FT /note="I -> V (in dbSNP:rs11545035)"
FT /id="VAR_045836"
FT VARIANT 247
FT /note="M -> V"
FT /evidence="ECO:0000269|PubMed:23033978"
FT /id="VAR_069369"
FT MUTAGEN 99
FT /note="C->S: Reduces N-glycosylation of cysteine-proximal
FT acceptor sites; when associated with S-102."
FT /evidence="ECO:0000269|PubMed:25135935"
FT MUTAGEN 102
FT /note="C->S: Reduces N-glycosylation of cysteine-proximal
FT acceptor sites; when associated with S-99."
FT /evidence="ECO:0000269|PubMed:25135935"
FT HELIX 44..62
FT /evidence="ECO:0007829|PDB:4M91"
FT STRAND 64..67
FT /evidence="ECO:0007829|PDB:4M91"
FT HELIX 70..76
FT /evidence="ECO:0007829|PDB:4M91"
FT STRAND 84..91
FT /evidence="ECO:0007829|PDB:4M91"
FT HELIX 95..97
FT /evidence="ECO:0007829|PDB:4M91"
FT HELIX 100..118
FT /evidence="ECO:0007829|PDB:4M91"
FT STRAND 126..132
FT /evidence="ECO:0007829|PDB:4M91"
FT TURN 133..135
FT /evidence="ECO:0007829|PDB:4M91"
FT HELIX 137..142
FT /evidence="ECO:0007829|PDB:4M91"
FT STRAND 150..154
FT /evidence="ECO:0007829|PDB:4M91"
FT STRAND 156..158
FT /evidence="ECO:0007829|PDB:4M91"
FT HELIX 162..164
FT /evidence="ECO:0007829|PDB:4M91"
FT HELIX 168..171
FT /evidence="ECO:0007829|PDB:4M91"
FT HELIX 175..186
FT /evidence="ECO:0007829|PDB:4M91"
SQ SEQUENCE 348 AA; 39676 MW; 16D97CB1E00C5190 CRC64;
MGARGAPSRR RQAGRRLRYL PTGSFPFLLL LLLLCIQLGG GQKKKENLLA EKVEQLMEWS
SRRSIFRMNG DKFRKFIKAP PRNYSMIVMF TALQPQRQCS VCRQANEEYQ ILANSWRYSS
AFCNKLFFSM VDYDEGTDVF QQLNMNSAPT FMHFPPKGRP KRADTFDLQR IGFAAEQLAK
WIADRTDVHI RVFRPPNYSG TIALALLVSL VGGLLYLRRN NLEFIYNKTG WAMVSLCIVF
AMTSGQMWNH IRGPPYAHKN PHNGQVSYIH GSSQAQFVAE SHIILVLNAA ITMGMVLLNE
AATSKGDVGK RRIICLVGLG LVVFFFSFLL SIFRSKYHGY PYSDLDFE
//

67
Tests/SwissProt/sp001
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@ -1,67 +0,0 @@
ID N33_HUMAN STANDARD; PRT; 348 AA.
AC Q13454; Q14911; Q14912;
DT 15-JUL-1999 (Rel. 38, Created)
DT 15-JUL-1999 (Rel. 38, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE N33 PROTEIN.
GN N33.
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN [1]
RP SEQUENCE FROM N.A.
RX MEDLINE; 96299740.
RA MACGROGAN D., LEVY A., BOVA G.S., ISAACS W.B., BOOKSTEIN R.;
RT "Structure and methylation-associated silencing of a gene within a
RT homozygously deleted region of human chromosome band 8p22.";
RL Genomics 35:55-65(1996).
CC -!- SUBCELLULAR LOCATION: INTEGRAL MEMBRANE PROTEIN (POTENTIAL).
CC -!- ALTERNATIVE PRODUCTS: TWO ISOFORMS SEEM TO BE PRODUCED BY
CC ALTERNATIVE SPLICING.
CC -!- TISSUE SPECIFICITY: EXPRESSED IN MOST NONLYMPHOID CELLS AND
CC TISSUES EXAMINED, INCLUDING PROSTATE, LUNG, LIVER, AND COLON.
CC -!- SIMILARITY: BELONGS TO THE OST3 FAMILY.
DR MIM; 601385; -.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; U42349; AAB18374.1; -.
DR EMBL; U42359; AAB18375.1; -.
DR EMBL; U42350; AAB18375.1; JOINED.
DR EMBL; U42351; AAB18375.1; JOINED.
DR EMBL; U42352; AAB18375.1; JOINED.
DR EMBL; U42354; AAB18375.1; JOINED.
DR EMBL; U42355; AAB18375.1; JOINED.
DR EMBL; U42356; AAB18375.1; JOINED.
DR EMBL; U42357; AAB18375.1; JOINED.
DR EMBL; U42358; AAB18375.1; JOINED.
DR EMBL; U42360; AAB18376.1; -.
DR EMBL; U42350; AAB18376.1; JOINED.
DR EMBL; U42351; AAB18376.1; JOINED.
DR EMBL; U42352; AAB18376.1; JOINED.
DR EMBL; U42354; AAB18376.1; JOINED.
DR EMBL; U42355; AAB18376.1; JOINED.
DR EMBL; U42356; AAB18376.1; JOINED.
DR EMBL; U42357; AAB18376.1; JOINED.
DR EMBL; U42358; AAB18376.1; JOINED.
KW Transmembrane; Alternative splicing.
FT TRANSMEM 20 40 POTENTIAL.
FT TRANSMEM 197 217 POTENTIAL.
FT TRANSMEM 222 242 POTENTIAL.
FT TRANSMEM 277 297 POTENTIAL.
FT TRANSMEM 313 333 POTENTIAL.
FT VARSPLIC 344 348 DLDFE -> FLIK (IN FORM 2).
SQ SEQUENCE 348 AA; 39676 MW; 75818910 CRC32;
MGARGAPSRR RQAGRRLRYL PTGSFPFLLL LLLLCIQLGG GQKKKENLLA EKVEQLMEWS
SRRSIFRMNG DKFRKFIKAP PRNYSMIVMF TALQPQRQCS VCRQANEEYQ ILANSWRYSS
AFCNKLFFSM VDYDEGTDVF QQLNMNSAPT FMHFPPKGRP KRADTFDLQR IGFAAEQLAK
WIADRTDVHI RVFRPPNYSG TIALALLVSL VGGLLYLRRN NLEFIYNKTG WAMVSLCIVF
AMTSGQMWNH IRGPPYAHKN PHNGQVSYIH GSSQAQFVAE SHIILVLNAA ITMGMVLLNE
AATSKGDVGK RRIICLVGLG LVVFFFSFLL SIFRSKYHGY PYSDLDFE
//

63
Tests/SwissProt/sp002
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@ -1,63 +0,0 @@
ID CSP_MOUSE STANDARD; PRT; 198 AA.
AC P54101;
DT 01-OCT-1996 (Rel. 34, Created)
DT 01-OCT-1996 (Rel. 34, Last sequence update)
DT 15-JUL-1998 (Rel. 36, Last annotation update)
DE CYSTEINE STRING PROTEIN (CSP).
GN CSP.
OS Mus musculus (Mouse), and Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.
RN [1]
RP SEQUENCE FROM N.A.
RC SPECIES=MOUSE; TISSUE=BRAIN;
RA QIN N., LIN T., BIRNBAUMER L.;
RL Submitted (OCT-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP SEQUENCE FROM N.A.
RC SPECIES=RAT; STRAIN=SPRAGUE-DAWLEY; TISSUE=BRAIN;
RX MEDLINE; 95223109.
RA MASTROGIACOMO A., GUNDERSEN C.B.;
RT "The nucleotide and deduced amino acid sequence of a rat cysteine
RT string protein.";
RL Brain Res. Mol. Brain Res. 28:12-18(1995).
RN [3]
RP SEQUENCE FROM N.A.
RC SPECIES=RAT; STRAIN=TISSUE=BRAIN;
RX MEDLINE; 96188189.
RA BRAUN J.E., SCHELLER R.H.;
RT "Cysteine string protein, a DnaJ family member, is present on diverse
RT secretory vesicles.";
RL Neuropharmacology 34:1361-1369(1995).
CC -!- FUNCTION: MAY HAVE AN IMPORTANT ROLE IN PRESYNAPTIC FUNCTION.
CC -!- SUBUNIT: HOMODIMER (PROBABLE).
CC -!- TISSUE SPECIFICITY: BRAIN. PREDOMINANTLY ASSOCIATED WITH NERVE
CC ENDINGS AND SYNAPTIC VESICLES.
CC -!- PTM: FATTY ACYLATED.
CC -!- SIMILARITY: CONTAINS A DNAJ-LIKE DOMAIN.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; U39320; AAA81372.1; -.
DR EMBL; S81917; AAB36303.1; -.
DR EMBL; AF032115; AAB87080.1; -.
DR HSSP; P25685; 1HDJ.
DR MGD; MGI:892995; CSP.
DR PFAM; PF00226; DnaJ; 1.
DR PROSITE; PS00636; DNAJ_1; 1.
DR PROSITE; PS50076; DNAJ_2; 1.
KW Lipoprotein.
FT DOMAIN 13 82 DNAJ-LIKE.
FT DOMAIN 118 128 POLY-CYS.
SQ SEQUENCE 198 AA; 22100 MW; 9DF0142B CRC32;
MADQRQRSLS TSGESLYHVL GLDKNATSDD IKKSYRKLAL KYHPDKNPDN PEAADKFKEI
NNAHAILTDA TKRNIYDKYG SLGLYVAEQF GEENVNTYFV LSSWWAKALF VVCGLLTCCY
CCCCLCCCFN CCCGKCKPKA PEGEETEFYV SPEDLEAQLQ SDEREATDTP IVIQPASATE
TTQLTADSHP SYHTDGFN
//

166
Tests/SwissProt/sp003
View File

@ -1,166 +0,0 @@
ID 143E_HUMAN STANDARD; PRT; 255 AA.
AC P42655; P29360; Q63631;
DT 01-NOV-1995 (REL. 32, CREATED)
DT 01-NOV-1995 (REL. 32, LAST SEQUENCE UPDATE)
DT 15-DEC-1998 (REL. 37, LAST ANNOTATION UPDATE)
DE 14-3-3 PROTEIN EPSILON (MITOCHONDRIAL IMPORT STIMULATION FACTOR L
DE SUBUNIT) (PROTEIN KINASE C INHIBITOR PROTEIN-1) (KCIP-1) (14-3-3E).
GN YWHAE.
OS HOMO SAPIENS (HUMAN), RATTUS NORVEGICUS (RAT), MUS MUSCULUS (MOUSE),
OS BOS TAURUS (BOVINE), AND OVIS ARIES (SHEEP).
OC EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; MAMMALIA; EUTHERIA;
OC PRIMATES; CATARRHINI; HOMINIDAE; HOMO.
RN [1]
RP SEQUENCE FROM N.A.
RC SPECIES=HUMAN;
RX MEDLINE; 95372385.
RA CONKLIN D.S., GALAKTIONOV K., BEACH D.;
RT "14-3-3 proteins associate with cdc25 phosphatases.";
RL PROC. NATL. ACAD. SCI. U.S.A. 92:7892-7896(1995).
RN [2]
RP SEQUENCE FROM N.A.
RC SPECIES=HUMAN; TISSUE=HEART;
RA LUK S.C.W., LEE C.Y., WAYE M.M.Y.;
RL SUBMITTED (JUN-1995) TO EMBL/GENBANK/DDBJ DATA BANKS.
RN [3]
RP SEQUENCE FROM N.A.
RC SPECIES=HUMAN;
RX MEDLINE; 96300316.
RA JIN D.Y., LYU M.S., KOZAK C.A., JEANG K.T.;
RT "Function of 14-3-3 proteins.";
RL NATURE 382:308-308(1996).
RN [4]
RP SEQUENCE FROM N.A.
RC SPECIES=HUMAN; TISSUE=LIVER;
RX MEDLINE; 97011338.
RA CHONG S.S., TANIGAMI A., ROSCHKE A.V., LEDBETTER D.H.;
RT "14-3-3 epsilon has no homology to LIS1 and lies telomeric to it on
RT chromosome 17p13.3 outside the Miller-Dieker syndrome chromosome
RT region.";
RL GENOME RES. 6:735-741(1996).
RN [5]
RP SEQUENCE FROM N.A.
RC SPECIES=HUMAN;
RA TANIGAMI A., CHONG S.S., LEDBETTER D.H.;
RT "14-3-3 epsilon genomic sequence.";
RL SUBMITTED (AUG-1998) TO EMBL/GENBANK/DDBJ DATA BANKS.
RN [6]
RP SEQUENCE FROM N.A.
RC SPECIES=RAT, AND SHEEP; TISSUE=PINEAL GLAND;
RX MEDLINE; 94296566.
RA ROSEBOOM P.H., WELLER J.L., BABILA T., AITKEN A., SELLERS L.A.,
RA MOFFET J.R., NAMBOODIRI M.A., KLEIN D.C.;
RT "Cloning and characterization of the epsilon and zeta isoforms of the
RT 14-3-3 proteins.";
RL DNA CELL BIOL. 13:629-640(1994).
RN [7]
RP SEQUENCE FROM N.A.
RC SPECIES=RAT; TISSUE=LIVER;
RX MEDLINE; 95122474.
RA ALAM R., HACHIYA N., SAKAGUCHI M., SHUN-ICHIRO K., IWANAGA S.,
RA KITAJIMA M., MIHARA K., OMURA T.;
RT "cDNA cloning and characterization of mitochondrial import
RT stimulation factor (MSF) purified from rat liver cytosol.";
RL J. BIOCHEM. 116:416-425(1994).
RN [8]
RP SEQUENCE FROM N.A.
RC SPECIES=RAT; TISSUE=BRAIN;
RX MEDLINE; 96280718.
RA GAO L., GU X.B., YU D.S., YU R.K., ZENG G.;
RT "Association of a 14-3-3 protein with CMP-NeuAc:GM1 alpha 2,3-
RT sialyltransferase.";
RL BIOCHEM. BIOPHYS. RES. COMMUN. 224:103-107(1996).
RN [9]
RP SEQUENCE FROM N.A.
RC SPECIES=MOUSE; STRAIN=SWISS; TISSUE=KIDNEY;
RX MEDLINE; 95269876.
RA MCCONNELL J.E., ARMSTRONG J.F., BARD J.B.;
RT "The mouse 14-3-3 epsilon isoform, a kinase regulator whose
RT expression pattern is modulated in mesenchyme and neuronal
RT differentiation.";
RL DEV. BIOL. 169:218-228(1995).
RN [10]
RP SEQUENCE FROM N.A.
RC SPECIES=MOUSE; STRAIN=129/SV;
RA TAKIHARA Y., IRIE K., NOMURA M., MOTALEB M., MATSUMOTO K.,
RA SHIMADA K.;
RL SUBMITTED (SEP-1996) TO EMBL/GENBANK/DDBJ DATA BANKS.
RN [11]
RP SEQUENCE FROM N.A.
RC SPECIES=BOVINE;
RA JONES J.M., NIIKURA T., PINKE R.M., GUO W., MOLDAY L., LEYKAM J.,
RA MCCONNELL D.G.;
RT "Expression of 14-3-3 proteins in bovine retinal photoreceptors.";
RL SUBMITTED (JAN-1998) TO EMBL/GENBANK/DDBJ DATA BANKS.
RN [12]
RP SEQUENCE OF 1-152; 165-184 AND 216-255.
RC SPECIES=SHEEP; TISSUE=BRAIN;
RX MEDLINE; 92283271.
RA TOKER A., SELLERS L.A., AMESS B., PATEL Y., HARRIS A., AITKEN A.;
RT "Multiple isoforms of a protein kinase C inhibitor (KCIP-1/14-3-3)
RT from sheep brain. Amino acid sequence of phosphorylated forms.";
RL EUR. J. BIOCHEM. 206:453-461(1992).
RN [13]
RP SEQUENCE OF 1-23 AND 125-140.
RC SPECIES=SHEEP; TISSUE=BRAIN;
RX MEDLINE; 90345949.
RA TOKER A., ELLIS C.A., SELLERS L.A., AITKEN A.;
RT "Protein kinase C inhibitor proteins. Purification from sheep brain
RT and sequence similarity to lipocortins and 14-3-3 protein.";
RL EUR. J. BIOCHEM. 191:421-429(1990).
CC -!- FUNCTION: ACTIVATES TYROSINE AND TRYPTOPHAN HYDROXYLASES IN THE
CC PRESENCE OF CA(2+)/CALMODULIN-DEPENDENT PROTEIN KINASE II, AND
CC STRONGLY ACTIVATES PROTEIN KINASE C. IS PROBABLY A MULTIFUNCTIONAL
CC REGULATOR OF THE CELL SIGNALING PROCESSES MEDIATED BY BOTH
CC KINASES.
CC -!- SUBUNIT: HOMODIMER.
CC -!- SUBCELLULAR LOCATION: CYTOPLASMIC.
CC -!- TISSUE SPECIFICITY: 14-3-3 PROTEINS ARE LOCALIZED IN NEURONS, AND
CC ARE AXONALLY TRANSPORTED TO THE NERVE TERMINALS. THEY MAY BE ALSO
CC PRESENT, AT LOWER LEVELS, IN VARIOUS OTHER EUKARYOTIC TISSUES.
CC -!- SIMILARITY: BELONGS TO THE 14-3-3 FAMILY.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; U28936; G984319; -.
DR EMBL; U20972; G902787; -.
DR EMBL; U43399; G1184725; -.
DR EMBL; U54778; G1561719; -.
DR EMBL; AB017103; D1033501; -.
DR EMBL; AB017098; D1033501; JOINED.
DR EMBL; AB017099; D1033501; JOINED.
DR EMBL; AB017100; D1033501; JOINED.
DR EMBL; AB017101; D1033501; JOINED.
DR EMBL; AB017102; D1033501; JOINED.
DR EMBL; M84416; G294504; -.
DR EMBL; D30739; G487918; -.
DR EMBL; Z19599; G57966; -.
DR EMBL; U53882; G1469948; -.
DR EMBL; L07914; G530049; -.
DR EMBL; D87663; G1526545; -.
DR EMBL; AF043735; G3676399; -.
DR PIR; S10806; S10806.
DR PIR; S10807; S10807.
DR MGD; MGI:894689; YWHAE.
DR PROSITE; PS00796; 1433_1; 1.
DR PROSITE; PS00797; 1433_2; 1.
DR PFAM; PF00244; 14-3-3; 1.
KW BRAIN; NEURONE; ACETYLATION; MULTIGENE FAMILY.
FT MOD_RES 1 1 ACETYLATION.
FT CONFLICT 73 73 K -> T (IN REF. 8).
FT CONFLICT 120 120 F -> S (IN REF. 8).
FT CONFLICT 123 123 K -> Y (IN REF. 8).
FT CONFLICT 129 129 H -> Y (IN REF. 13).
SQ SEQUENCE 255 AA; 29174 MW; 40A43E62 CRC32;
MDDREDLVYQ AKLAEQAERY DEMVESMKKV AGMDVELTVE ERNLLSVAYK NVIGARRASW
RIISSIEQKE ENKGGEDKLK MIREYRQMVE TELKLICCDI LDVLDKHLIP AANTGESKVF
YYKMKGDYHR YLAEFATGND RKEAAENSLV AYKAASDIAM TELPPTHPIR LGLALNFSVF
YYEILNSPDR ACRLAKAAFD DAIAELDTLS EESYKDSTLI MQLLRDNLTL WTSDMQGDGE
EQNKEALQDV EDENQ
//

49
Tests/SwissProt/sp005
View File

@ -1,49 +0,0 @@
ID NU3M_BALPH STANDARD; PRT; 115 AA.
AC P24973;
DT 01-MAR-1992 (Rel. 21, Created)
DT 01-MAR-1992 (Rel. 21, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 3 (EC 1.6.5.3).
GN MTND3 OR ND3 OR NADH3.
OS Balaenoptera physalus (Finback whale) (Common rorqual), and
OS Balaenoptera musculus (Blue whale).
OG Mitochondrion.
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Cetartiodactyla; Cetacea; Mysticeti; Balaenopteridae;
OC Balaenoptera.
RN [1]
RP SEQUENCE FROM N.A.
RC SPECIES=B.PHYSALUS; STRAIN=ISOLATE=NO 27, ANNO 1987; TISSUE=LIVER;
RX MEDLINE; 92139449.
RA ARNASON U., GULLBERG A., WIDEGREN B.;
RT "The complete nucleotide sequence of the mitochondrial DNA of the fin
RT whale, Balaenoptera physalus.";
RL J. Mol. Evol. 33:556-568(1991).
RN [2]
RP SEQUENCE FROM N.A.
RC SPECIES=B.MUSCULUS;
RX MEDLINE; 94141932.
RA ARNASON U., GULLBERG A.;
RT "Comparison between the complete mtDNA sequences of the blue and the
RT fin whale, two species that can hybridize in nature.";
RL J. Mol. Evol. 37:312-322(1993).
CC -!- CATALYTIC ACTIVITY: NADH + UBIQUINONE = NAD(+) + UBIQUINOL.
CC -!- SIMILARITY: BELONGS TO THE COMPLEX I SUBUNIT 3 FAMILY.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; X61145; CAA43446.1; -.
DR EMBL; X72204; CAA51002.1; -.
DR PIR; S41827; S41827.
DR PFAM; PF00507; oxidored_q4; 1.
KW Oxidoreductase; NAD; Ubiquinone; Mitochondrion.
SQ SEQUENCE 115 AA; 13022 MW; ACF02965 CRC32;
MNLLLTLLTN TTLALLLVFI AFWLPQLNVY AEKTSPYECG FDPMGSARLP FSMKFFLVAI
TFLLFDLEIA LLLPLPWAIQ SNNLNTMLTM ALFLISLLAA SLAYEWTQEG LEWAE
//

47
Tests/SwissProt/sp006
View File

@ -1,47 +0,0 @@
ID TCMO_STRGA STANDARD; PRT; 339 AA.
AC P39896;
DT 01-FEB-1995 (REL. 31, CREATED)
DT 01-FEB-1995 (REL. 31, LAST SEQUENCE UPDATE)
DT 01-NOV-1995 (REL. 32, LAST ANNOTATION UPDATE)
DE TETRACENOMYCIN POLYKETIDE SYNTHESIS 8-O-METHYL TRANSFERASE TCMO
DE (EC 2.1.1.-).
GN TCMO.
OS STREPTOMYCES GLAUCESCENS.
OC BACTERIA; FIRMICUTES; ACTINOBACTERIA; ACTINOBACTERIDAE;
OC ACTINOMYCETALES; STREPTOMYCINEAE; STREPTOMYCETACEAE; STREPTOMYCES.
RN [1]
RP SEQUENCE FROM N.A.
RC STRAIN=GLA.0;
RX MEDLINE; 92193265.
RA SUMMERS R.G., WENDT-PIENKOWSKI E., MOTAMEDI H., HUTCHINSON C.R.;
RT "Nucleotide sequence of the tcmII-tcmIV region of the tetracenomycin
RT C biosynthetic gene cluster of Streptomyces glaucescens and evidence
RT that the tcmN gene encodes a multifunctional
RT cyclase-dehydratase-O-methyl transferase.";
RL J. BACTERIOL. 174:1810-1820(1992).
CC TETRACENOMYCIN B3 TO TETRACENOMYCIN E. METHYLATES AS WELL TCM D3
CC INTO 8-O-METHYL-TCM D3, A SIDE REACTION.
CC -!- PATHWAY: SECOND STEP IN THE BIOSYNTHESIS OF THE POLYKETIDE
CC ANTIBIOTIC TETRACENOMYCIN C (TCM C) FROM TCM D3.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; M80674; G153500; -.
DR PIR; S27697; S27697.
DR PIR; C42276; C42276.
DR PFAM; PF00891; Methyltransf; 1.
KW ANTIBIOTIC BIOSYNTHESIS; TRANSFERASE; METHYLTRANSFERASE.
SQ SEQUENCE 339 AA; 37035 MW; 848B7337 CRC32;
MTPHTHVRGP GDILQLTMAF YGSRALISAV ELDLFTLLAG KPLPLGELCE RAGIHPRGAR
DFLDALVALG LLEREGEDTY RNSPAADRHL DRRKPGYVGG YARLADTKLF PVWARLTEAL
RTGEKQVPSQ GGFFGGYADP EAARGFLGAM DAVNGGVGHS LAGALDWTEY SSFVDLGGAR
GNLAAHLHRA HPHLRATCFD LPEMEPFFQE HMKSLETTDQ VRFAGGDFFT DPLPRADVFI
VGHILHYFGL RQREALIARI HQALTPGGAV LVYDRMIDDD RRSAALSLLG SLNMLLTSDE
GREYTPAECV RWLSDAGFTD VRTTAVSGPD TLAIGRKPR
//

60
Tests/SwissProt/sp007
View File

@ -1,60 +0,0 @@
ID CLD1_HUMAN STANDARD; PRT; 211 AA.
AC O95832;
DT 15-FEB-2000 (Rel. 39, Created)
DT 15-FEB-2000 (Rel. 39, Last sequence update)
DT 15-FEB-2000 (Rel. 39, Last annotation update)
DE CLAUDIN-1 (SENESCENCE-ASSOCIATED EPITHELIAL MEMBRANE PROTEIN).
GN CLDN1 OR CLD1 OR SEMP1.
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN [1]
RP SEQUENCE FROM N.A.
RX MEDLINE; 99132301. [NCBI, ExPASy, Israel, Japan]
RA Swisshelm K.L., Machl A., Planitzer S., Robertson R., Kubbies M.,
RA Hosier S.;
RT "SEMP1, a senescence-associated cDNA isolated from human mammary
RT epithelial cells, is a member of an epithelial membrane protein
RT superfamily.";
RL Gene 226:285-295(1999).
RN [2]
RP SEQUENCE FROM N.A.
RA Mitic L.M., Anderson J.M.;
RT "Human claudin-1 isolated from Caco-2 mRNA.";
RL Submitted (DEC-1998) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: COMPONENT OF TIGHT JUNCTION (TJ) STRANDS.
CC -!- SUBCELLULAR LOCATION: INTEGRAL MEMBRANE PROTEIN.
CC -!- SIMILARITY: BELONGS TO THE CLAUDIN FAMILY.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; AF101051; AAD16433.1; -. [EMBL / GenBank / DDBJ] [CoDingSequence]
DR EMBL; AF115546; AAD22962.1; -. [EMBL / GenBank / DDBJ] [CoDingSequence]
DR GeneCards; CLDN1.
DR MIM; 603718; -.
DR PROSITE; PS01346; CLAUDIN; 1.
DR PRODOM [Domain structure / List of seq. sharing at least 1 domain]
DR BLOCKS; O95832.
DR DOMO; O95832.
DR PROTOMAP; O95832.
DR PRESAGE; O95832.
DR SWISS-2DPAGE; GET REGION ON 2D PAGE.
KW Tight junction; Transmembrane.
FT TRANSMEM 8 28 POTENTIAL.
FT TRANSMEM 82 102 POTENTIAL.
FT TRANSMEM 116 136 POTENTIAL.
FT TRANSMEM 164 184 POTENTIAL.
FT CONFLICT 62 62 I -> V (IN REF. 2).
FT CONFLICT 135 135 V -> A (IN REF. 2).
SQ SEQUENCE 211 AA; 22744 MW; 07269000E6C214F0 CRC64;
MANAGLQLLG FILAFLGWIG AIVSTALPQW RIYSYAGDNI VTAQAMYEGL WMSCVSQSTG
QIQCKVFDSL LNLSSTLQAT RALMVVGILL GVIAIFVATV GMKCMKCLED DEVQKMRMAV
IGGAIFLLAG LAILVATAWY GNRIVQEFYD PMTPVNARYE FGQALFTGWA AASLCLLGGA
LLCCSCPRKT TSYPTPRPYP KPAPSSGKDY V
//

365
Tests/SwissProt/sp008
View File

@ -1,365 +0,0 @@
ID 1A02_HUMAN STANDARD; PRT; 365 AA.
AC P01892; P06338; P30514; P30444; P30445; P30446; Q29680; Q29899;
AC Q95352; Q29837; Q95380;
DT 21-JUL-1986 (Rel. 01, Created)
DT 13-AUG-1987 (Rel. 05, Last sequence update)
DT 15-FEB-2000 (Rel. 39, Last annotation update)
DE HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN PRECURSOR.
GN HLA-A OR HLAA.
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN [1]
RP SEQUENCE FROM N.A. (A*0201).
RX MEDLINE; 85132727.
RA Koller B.H., Orr H.T.;
RT "Cloning and complete sequence of an HLA-A2 gene: analysis of two
RT HLA-A alleles at the nucleotide level.";
RL J. Immunol. 134:2727-2733(1985).
RN [2]
RP SEQUENCE FROM N.A. (A*0201).
RX MEDLINE; 89122144.
RA Cianetti L., Testa U., Scotto L., la Valle R., Simeone A.,
RA Boccoli G., Giannella G., Peschle C., Boncinelli E.;
RT "Three new class I HLA alleles: structure of mRNAs and alternative
RT mechanisms of processing.";
RL Immunogenetics 29:80-91(1989).
RN [3]
RP SEQUENCE FROM N.A. (A*0201).
RX MEDLINE; 90207291.
RA Ennis P.D., Zemmour J., Salter R.D., Parham P.;
RT "Rapid cloning of HLA-A,B cDNA by using the polymerase chain
RT reaction: frequency and nature of errors produced in amplification.";
RL Proc. Natl. Acad. Sci. U.S.A. 87:2833-2837(1990).
RN [4]
RP SEQUENCE FROM N.A. (A*0201/A*0211/A*0212).
RX MEDLINE; 92269955.
RA Belich M.P., Madrigal J.A., Hildebrand W.H., Zemmour J.,
RA Williams R.C., Luz R., Petzl-Erler M.L., Parham P.;
RT "Unusual HLA-B alleles in two tribes of Brazilian Indians.";
RL Nature 357:326-329(1992).
RN [5]
RP SEQUENCE OF 39-365 FROM N.A. (A*0201).
RX MEDLINE; 85230571.
RA Krangel M.S.;
RT "Unusual RNA splicing generates a secreted form of HLA-A2 in a
RT mutagenized B lymphoblastoid cell line.";
RL EMBO J. 4:1205-1210(1985).
RN [6]
RP SEQUENCE OF 25-295 (A*0201).
RX MEDLINE; 80056745.
RA Orr H.T., Lopez de Castro J.A., Parham P., Ploegh H.L.,
RA Strominger J.L.;
RT "Comparison of amino acid sequences of two human histocompatibility
RT antigens, HLA-A2 and HLA-B7: location of putative alloantigenic
RT sites.";
RL Proc. Natl. Acad. Sci. U.S.A. 76:4395-4399(1979).
RN [7]
RP REVISIONS (A*0201).
RX MEDLINE; 82247941.
RA Lopez de Castro J.A., Strominger J.L., Strong D.M., Orr H.T.;
RT "Structure of crossreactive human histocompatibility antigens HLA-A28
RT and HLA-A2: possible implications for the generation of HLA
RT polymorphism.";
RL Proc. Natl. Acad. Sci. U.S.A. 79:3813-3817(1982).
RN [8]
RP SEQUENCE OF 26-298 FROM N.A. (A*0202/A*0203).
RX MEDLINE; 87306734.
RA Mattson D.H., Handy D.E., Bradley D.A., Coligan J.E., Cowan E.P.,
RA Biddison W.E.;
RT "DNA sequences of the genes that encode the CTL-defined HLA-A2
RT variants M7 and DK1.";
RL Immunogenetics 26:190-192(1987).
RN [9]
RP SEQUENCE FROM N.A. (A*0203/A*0205).
RX MEDLINE; 87252273.
RA Holmes N., Ennis P., Wan A.M., Denney D.W., Parham P.;
RT "Multiple genetic mechanisms have contributed to the generation of
RT the HLA-A2/A28 family of class I MHC molecules.";
RL J. Immunol. 139:936-941(1987).
RN [10]
RP SEQUENCE FROM N.A. (A*0203/A*0205).
RA Domena J.D.;
RL Submitted (NOV-1993) to the EMBL/GenBank/DDBJ databases.
RN [11]
RP SEQUENCE OF 9-365 FROM N.A. (A*0204).
RX MEDLINE; 92039809.
RA Castano A.R., Lopez de Castro J.A.;
RT "Structure of the HLA-A*0204 antigen, found in South American
RT Indians. Spatial clustering of HLA-A2 subtype polymorphism.";
RL Immunogenetics 34:281-285(1991).
RN [12]
RP SEQUENCE OF 9-365 FROM N.A. (A*0204).
RX MEDLINE; 92269956.
RA Watkins D.I., McAdam S.N., Liu X., Stang C.R., Milford E.L.,
RA Levine C.G., Garber T.L., Dogon A.L., Lord C.I., Ghim S.H.,
RA Troup G.M., Hughes A.L., Letvin N.L.;
RT "New recombinant HLA-B alleles in a tribe of South American
RT Amerindians indicate rapid evolution of MHC class I loci.";
RL Nature 357:329-333(1992).
RN [13]
RP SEQUENCE FROM N.A. (A*0206).
RX MEDLINE; 89235215.
RA Parham P., Lawlor D.A., Lomen C.E., Ennis P.D.;
RT "Diversity and diversification of HLA-A,B,C alleles.";
RL J. Immunol. 142:3937-3950(1989).
RN [14]
RP PARTIAL SEQUENCE (A*0206).
RX MEDLINE; 86305811.
RA Ezquerra A., Domenech N., van der Poel J., Strominger J.L., Vega M.A.,
RA Lopez de Castro J.A.;
RT "Molecular analysis of an HLA-A2 functional variant CLA defined by
RT cytolytic T lymphocytes.";
RL J. Immunol. 137:1642-1649(1986).
RN [15]
RP PARTIAL SEQUENCE (A*0207).
RX MEDLINE; 88113844.
RA Domenech N., Ezquerra A., Castano R., Lopez de Castro J.A.;
RT "Structural analysis of HLA-A2.4 functional variant KNE. Implications
RT for the mapping of HLA-A2-specific T-cell epitopes.";
RL Immunogenetics 27:196-202(1988).
RN [16]
RP PARTIAL SEQUENCE (A*0208).
RX MEDLINE; 88314183.
RA Domenech N., Castano R., Goulmy E., Lopez de Castro J.A.;
RT "Molecular analysis of HLA-A2.4 functional variant KLO: close
RT structural and evolutionary relatedness to the HLA-A2.2 subtype.";
RL Immunogenetics 28:143-152(1988).
RN [17]
RP PARTIAL SEQUENCE (A*0209).
RX MEDLINE; 88186100.
RA Castano R., Ezquerra A., Domenech N., Lopez de Castro J.A.;
RT "An HLA-A2 population variant with structural polymorphism in the
RT alpha 3 region.";
RL Immunogenetics 27:345-355(1988).
RN [18]
RP SEQUENCE FROM N.A. (A*0210).
RX MEDLINE; 89122133.
RA Epstein H., Kennedy L., Holmes N.;
RT "An Oriental HLA-A2 subtype is closely related to a subset of
RT Caucasoid HLA-A2 alleles.";
RL Immunogenetics 29:112-116(1989).
RN [19]
RP SEQUENCE OF 9-365 FROM N.A. (A*0211).
RX MEDLINE; 92218010.
RA Castano A.R., Lopez de Castro J.A.;
RT "Structure of the HLA-A*0211 (A2.5) subtype: further evidence for
RT selection-driven diversification of HLA-A2 antigens.";
RL Immunogenetics 35:344-346(1992).
RN [20]
RP SEQUENCE FROM N.A. (A*0213).
RX MEDLINE; 94222455.
RA Barber D.F., Fernandez J.M., Lopez de Castro J.A.;
RT "Primary structure of a new HLA-A2 subtype: HLA-A*0213.";
RL Immunogenetics 39:378-378(1994).
RN [21]
RP SEQUENCE FROM N.A. (A*0216).
RX MEDLINE; 95278976.
RA Barouch D., Krausa P., Bodmer J., Browning M.J., McMichael A.J.;
RT "Identification of a novel HLA-A2 subtype, HLA-A*0216.";
RL Immunogenetics 41:388-388(1995).
RN [22]
RP SEQUENCE FROM N.A. (A*0217).
RC TISSUE=BLOOD;
RX MEDLINE; 95381236.
RA Selvakumar A., Granja C.B., Salazar M., Alosco S.M., Yunis E.J.,
RA Dupont B.;
RT "A novel subtype of A2 (A*0217) isolated from the South American
RT Indian B-cell line AMALA.";
RL Tissue Antigens 45:343-347(1995).
RN [23]
RP SEQUENCE FROM N.A. (A*0218).
RC TISSUE=BLOOD;
RA Kashiwase K., Tokunaga K., Ishikawa Y., Oohashi H., Hashimoto M.,
RA Akaza T., Tadokoro K., Juji T.;
RT "A new A2 sequence HLA-A2K from Japanese.";
RL Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases.
RN [24]
RP SEQUENCE FROM N.A. (A*0220).
RC TISSUE=BLOOD;
RX MEDLINE; 97161038.
RA Fleischhauer K., Zino E., Mazzi B., Severini G.M., Benazzi E.,
RA Bordignon C.;
RT "HLA-A*02 subtype distribution in Caucasians from northern Italy:
RT identification of A*0220.";
RL Tissue Antigens 48:673-679(1996).
RN [25]
RP SEQUENCE FROM N.A. (A*0221).
RC TISSUE=BLOOD;
RA Szmania S., Baxter-Lowe L.A.;
RT "Nucleotide sequence of a novel HLA-A2 gene.";
RL Submitted (APR-1996) to the EMBL/GenBank/DDBJ databases.
RN [26]
RP X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF A*0201.
RX MEDLINE; 88014204.
RA Bjorkman P.J., Saper M.A., Samraoui B., Bennett W.S.,
RA Strominger J.L., Wiley D.C.;
RT "Structure of the human class I histocompatibility antigen, HLA-A2.";
RL Nature 329:506-512(1987).
RN [27]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF A*0201.
RX MEDLINE; 91245570.
RA Saper M.A., Bjorkman P.J., Wiley D.C.;
RT "Refined structure of the human histocompatibility antigen HLA-A2 at
RT 2.6-A resolution.";
RL J. Mol. Biol. 219:277-319(1991).
CC -!- FUNCTION: INVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO
CC THE IMMUNE SYSTEM.
CC -!- SUBUNIT: DIMER OF ALPHA CHAIN AND A BETA CHAIN (BETA-2-
CC MICROGLOBULIN).
CC -!- POLYMORPHISM: THE FOLLOWING ALLELES OF A-2 ARE KNOWN: A*0201,
CC A*0202, A*0203, A*0204, A*0205, A*0206 (A2.4A), A*0207, A*0208,
CC A*0209, A*0210, A*0211 (A2.5), A*0212, A*0213 (A*02SLU), A*0216,
CC A*0217, A*0218 (A2K), A*0219, A*0220 AND A*0221. THE SEQUENCE
CC SHOWN IS THAT OF A*0201.
CC -!- CAUTION: REF.6 AND REF.7 SEQUENCES DIFFER FROM THAT SHOWN
CC EXTENSIVELY.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; K02883; AAA98727.1; -.
DR EMBL; M84379; AAA59606.1; -.
DR EMBL; X02457; CAA26297.1; -.
DR EMBL; M19670; AAA03683.1; -.
DR EMBL; M17690; AAB02120.1; -.
DR EMBL; U03863; AAA03604.1; -.
DR EMBL; M86404; -; NOT_ANNOTATED_CDS.
DR EMBL; X57954; CAA41022.1; ALT_SEQ.
DR EMBL; U03862; AAA03603.1; -.
DR EMBL; M24042; AAA59653.1; -.
DR EMBL; Z23071; CAA80612.1; -.
DR EMBL; M84377; AAA59603.1; -.
DR EMBL; X60764; -; NOT_ANNOTATED_CDS.
DR EMBL; M84378; AAA59604.1; -.
DR EMBL; Z27120; CAA81644.1; -.
DR EMBL; Z46633; CAA86602.1; -.
DR EMBL; U18930; AAA87076.1; -.
DR EMBL; D83515; BAA11935.1; -.
DR EMBL; X96724; CAA65501.1; -.
DR EMBL; U56825; AAB17465.1; -.
DR PIR; A02188; HLHUA2.
DR PIR; A02191; HLHU2A.
DR PIR; E35997; E35997.
DR PIR; S19020; S19020.
DR PIR; S23593; S23593.
DR PDB; 1HLA; 15-JUL-90.
DR PDB; 3HLA; 15-APR-90.
DR PDB; 1HHG; 31-OCT-93.
DR PDB; 1HHH; 31-OCT-93.
DR PDB; 1HHI; 31-OCT-93.
DR PDB; 1HHJ; 31-OCT-93.
DR PDB; 1HHK; 31-OCT-93.
DR PDB; 1AQD; 28-JAN-98.
DR MIM; 142800; -.
DR PROSITE; PS00290; IG_MHC; 1.
DR PFAM; PF00047; ig; 1.
DR PFAM; PF00129; MHC_I; 1.
KW MHC I; Transmembrane; Glycoprotein; Signal; Polymorphism;
KW 3D-structure.
FT SIGNAL 1 24
FT CHAIN 25 365 HLA CLASS I HISTOCOMPATIBILITY ANTIGEN,
FT A-2 ALPHA CHAIN.
FT DOMAIN 25 114 EXTRACELLULAR ALPHA-1.
FT DOMAIN 115 206 EXTRACELLULAR ALPHA-2.
FT DOMAIN 207 298 EXTRACELLULAR ALPHA-3.
FT DOMAIN 299 308 CONNECTING PEPTIDE.
FT TRANSMEM 309 332
FT DOMAIN 333 365 CYTOPLASMIC TAIL.
FT CARBOHYD 110 110
FT DISULFID 125 188
FT DISULFID 227 283
FT STRAND 27 36
FT STRAND 45 52
FT TURN 53 54
FT STRAND 55 61
FT TURN 62 63
FT STRAND 70 71
FT HELIX 74 76
FT TURN 77 78
FT HELIX 81 108
FT TURN 109 110
FT TURN 113 114
FT STRAND 118 127
FT TURN 129 130
FT STRAND 133 142
FT TURN 143 144
FT STRAND 145 150
FT TURN 152 153
FT STRAND 157 159
FT TURN 163 163
FT HELIX 164 173
FT TURN 174 175
FT HELIX 176 185
FT TURN 186 186
FT HELIX 187 198
FT TURN 199 199
FT HELIX 200 203
FT TURN 204 204
FT STRAND 207 207
FT STRAND 210 219
FT TURN 220 221
FT STRAND 222 233
FT STRAND 238 243
FT TURN 244 245
FT STRAND 246 247
FT HELIX 249 251
FT STRAND 253 254
FT STRAND 258 259
FT STRAND 265 274
FT TURN 275 276
FT HELIX 278 280
FT STRAND 281 286
FT TURN 288 289
FT STRAND 294 297
FT VARIANT 33 33 F -> Y (IN A*0205, A*0206, A*0208, A*0210
FT AND A*0221).
FT /FTId=VAR_004334.
FT VARIANT 54 54 D -> N (IN A*0221).
FT /FTId=VAR_004335.
FT VARIANT 67 67 Q -> R (IN A*0202, A*0205, AND A*0208).
FT /FTId=VAR_004336.
FT VARIANT 90 90 K -> N (IN A*0208 AND A*0220).
FT /FTId=VAR_004337.
FT VARIANT 97 98 TH -> ID (IN A*0211).
FT /FTId=VAR_004338.
FT VARIANT 119 119 V -> L (IN A*0202, A*0205, A*0208 AND
FT A*0217).
FT /FTId=VAR_004339.
FT VARIANT 121 121 R -> M (IN A*0204 AND A*0217).
FT /FTId=VAR_004340.
FT VARIANT 123 123 Y -> C (IN A*0207 AND A*0218).
FT /FTId=VAR_004341.
FT VARIANT 123 123 Y -> F (IN A*0210 AND A*0217).
FT /FTId=VAR_004342.
FT VARIANT 131 131 W -> G (IN A*0210).
FT /FTId=VAR_004343.
FT VARIANT 162 162 M -> K (IN A*0218).
FT /FTId=VAR_004344.
FT VARIANT 173 173 A -> T (IN A*0203).
FT /FTId=VAR_004345.
FT VARIANT 176 176 V -> E (IN A*0203 AND A*0213).
FT /FTId=VAR_004346.
FT VARIANT 180 180 L -> W (IN A*0202, A*0203, A*0205 AND
FT A*0208).
FT /FTId=VAR_004347.
FT VARIANT 180 180 L -> Q (IN A*0212 AND A*0213).
FT /FTId=VAR_004348.
FT VARIANT 187 187 T -> E (IN A*0216).
FT /FTId=VAR_004349.
FT VARIANT 260 260 A -> E (IN A*0209).
FT /FTId=VAR_004350.
SQ SEQUENCE 365 AA; 40922 MW; B54A97B24B337C08 CRC64;
MAVMAPRTLV LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDGETRK VKAHSQTHRV DLGTLRGYYN QSEAGSHTVQ
RMYGCDVGSD WRFLRGYHQY AYDGKDYIAL KEDLRSWTAA DMAAQTTKHK WEAAHVAEQL
RAYLEGTCVE WLRRYLENGK ETLQRTDAPK THMTHHAVSD HEATLRCWAL SFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHVQHEGL PKPLTLRWEP
SSQPTIPIVG IIAGLVLFGA VITGAVVAAV MWRRKSSDRK GGSYSQAASS DSAQGSDVSL
TACKV
//

53
Tests/SwissProt/sp009
View File

@ -1,53 +0,0 @@
ID CHS3_BROFI STANDARD; PRT; 394 AA.
AC O23729;
DT 15-JUL-1999 (Rel. 38, Created)
DT 15-JUL-1999 (Rel. 38, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE CHALCONE SYNTHASE 3 (EC 2.3.1.74) (NARINGENIN-CHALCONE SYNTHASE 3).
GN CHS3.
OS Bromheadia finlaysoniana (Orchid).
OC Eukaryota; Viridiplantae; Embryophyta; Tracheophyta; Spermatophyta;
OC Magnoliophyta; Liliopsida; Asparagales; Orchidaceae; Bromheadia.
OX NCBI_TaxID=41205;
RN [1]
RP SEQUENCE FROM N.A.
RC TISSUE=Flower;
RA Liew C.F., Lim S.H., Loh C.S., Goh C.J.;
RT "Molecular cloning and sequence analysis of chalcone synthase cDNAs of
RT Bromheadia finlaysoniana.";
RL Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: THE PRIMARY PRODUCT OF THIS ENZYME IS 4,2',4',6'-
CC TETRAHYDROXYCHALCONE (ALSO TERMED NARINGENIN-CHALCONE OR CHALCONE)
CC WHICH CAN UNDER SPECIFIC CONDITIONS SPONTANEOUSLY ISOMERIZE INTO
CC NARINGENIN.
CC -!- CATALYTIC ACTIVITY: 3 MALONYL-COA + 4-COUMAROYL-COA = 4 COA +
CC NARINGENIN-CHALCONE + 3 CO(2).
CC -!- PATHWAY: PART OF THE BIOSYNTHETIC PATHWAY FOR ALL CLASSES OF
CC FLAVONOIDS, A LARGE CLASS OF SECONDARY PLANT METABOLITES, MANY
CC OF WHICH ARE BRIGHTLY COLORED.
CC -!- SIMILARITY: BELONGS TO THE CHALCONE/STILBENE SYNTHASES FAMILY.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; AF007097; AAB62874.1; -.
DR InterPro; IPR001099; -.
DR Pfam; PF00195; Chal_stil_synt; 1.
DR PROSITE; PS00441; CHALCONE_SYNTH; 1.
KW Flavonoid biosynthesis; Transferase; Acyltransferase;
KW Multigene family.
FT ACT_SITE 165 165 BY SIMILARITY.
SQ SEQUENCE 394 AA; 42941 MW; 2F8D14AF4870BBB2 CRC64;
MAPAMEEIRQ AQRAEGPAAV LAIGTSTPPN ALYQADYPDY YFRITKSEHL TELKEKFKRM
CDKSMIKKRY MYLTEEILKE NPNICAFMAP SLDARQDIVV TEVPKLAKEA AVRAIKEWGH
PKSRITHLIF CTTSGIDMPG ADYQLTRLLG LRPSVNRFML YQQGCFAGGT VLRLAKDLAE
NNAGARVLVV CSEITAVTFR GPSESHLDSL VGQALFGDGA AAIIVGSDPD SATERPLFQL
VSASQTILPE SEGAIDGHLR EIGLTFHLLK DVPGLISKNI QKCLLDAFKP LGVHDWNSIF
WIAHPGGPAI LDQVEIKLGL KAEKLAASRN VLAEYGNMSS ACVLFILDEM RRRSAEAGQA
TTGEGLEWGV LFGFGPGLTV ETIVLRSVPI AGAE
//

140
Tests/SwissProt/sp010
View File

@ -1,140 +0,0 @@
ID 5H4_HUMAN STANDARD; PRT; 388 AA.
AC Q13639; Q9UBM6; Q9UQR6; Q9UE22; Q9UE23; Q9UBT4; Q9NY73;
DT 01-NOV-1997 (Rel. 35, Created)
DT 01-OCT-2000 (Rel. 40, Last sequence update)
DT 01-OCT-2000 (Rel. 40, Last annotation update)
DE 5-HYDROXYTRYPTAMINE 4 RECEPTOR (5-HT-4) (SEROTONIN RECEPTOR) (5-HT4).
GN HTR4.
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP SEQUENCE FROM N.A. (ISOFORMS 5-HT4(A); 5-HT4(B); 5-HT4(C); 5-HT4(D)).
RC TISSUE=Gut;
RX PubMed=9603189;
RA Blondel O., Gastineau M., Dahmoune Y., Langlois M., Fischmeister R.;
RT "Cloning, expression, and pharmacology of four human 5-
RT hydroxytryptamine receptor isoforms produced by alternative splicing
RT in the carboxyl terminus.";
RL J. Neurochem. 70:2252-2261(1998).
RN [2]
RP SEQUENCE FROM N.A. (ISOFORMS 5-HT4(A) AND 5HT4(B)).
RC TISSUE=Brain;
RA Van den Wyngaert I., Gommeren W., Jurzak M., Verhasselt P., Gordon R.,
RA Leysen J., Luyten W., Bender E.;
RT "Cloning and expression of 5-HT4 receptor species and splice
RT variants.";
RL Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP SEQUENCE FROM N.A. (ISOFORM 5-HT4(A)).
RC TISSUE=Heart;
RX PubMed=9351641;
RA Claeysen S., Faye P., Sebben M., Lemaire S., Bockaert J., Dumuis A.;
RT "Cloning and expression of human 5-HT4S receptors. Effect of receptor
RT density on their coupling to adenylyl cyclase.";
RL NeuroReport 8:3189-3195(1997).
RN [4]
RP SEQUENCE FROM N.A. (ISOFORM 5-HT4(E)).
RC TISSUE=Brain;
RA Claeysen S., Sebben M., Becamel C., Bockaert J., Dumuis A.;
RT "Novel brain-specific 5-HT4 receptors splice variants show marked
RT constitutive activity: role of the c-terminal intracellular domain.";
RL Mol. Pharmacol. 55:0-0(1999).
RN [5]
RP SEQUENCE OF 10-388 FROM N.A. (ISOFORM 5-HT4(F)).
RX PubMed=10646498;
RA Bender E., Pindon A., van Oers I., Zhang Y.B., Gommeren W.,
RA Verhasselt P., Jurzak M., Leysen J., Luyten W.;
RT "Structure of the human serotonin 5-HT4 receptor gene and cloning of a
RT novel 5-HT4 splice variant.";
RL J. Neurochem. 74:478-489(2000).
RN [6]
RP SEQUENCE OF 112-255 FROM N.A.
RC TISSUE=Brain;
RX MEDLINE=95385798; PubMed=7656980;
RA Ullmer C., Schmuck K., Kalkman H.O., Lubbert H.;
RT "Expression of serotonin receptor mRNAs in blood vessels.";
RL FEBS Lett. 370:215-221(1995).
CC -!- FUNCTION: THIS IS ONE OF THE SEVERAL DIFFERENT RECEPTORS FOR
CC 5-HYDROXYTRYPTAMINE (SEROTONIN), A BIOGENIC HORMONE THAT FUNCTION
CC AS A NEUROTRANSMITTER, A HORMONE, AND A MITOGEN. THE ACTIVITY OF
CC THIS RECEPTOR IS MEDIATED BY G PROTEINS THAT STIMULATES ADENYLATE
CC CYCLASE.
CC -!- SUBCELLULAR LOCATION: INTEGRAL MEMBRANE PROTEIN.
CC -!- ALTERNATIVE PRODUCTS: AT LEAST 6 ISOFORMS; 5-HT4(A)/5-HT4S, 5-
CC HT4(B) (SHOWN HERE), 5-HT4(C), 5-HT4(D); 5-HT4(E) AND 5-HT4(F);
CC ARE PRODUCED BY ALTERNATIVE SPLICING.
CC -!- TISSUE SPECIFICITY: ISOFORM 5-HT4(A)IS EXPRESSED IN ILEUM, BRAIN,
CC AND ATRIUM, BUT NOT IN THE VENTRICLE.
CC -!- SIMILARITY: BELONGS TO FAMILY 1 OF G-PROTEIN COUPLED RECEPTORS.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; Y12505; CAA73107.1; -.
DR EMBL; Y12506; CAA73108.1; -.
DR EMBL; Y12507; CAA73109.1; -.
DR EMBL; Y10437; CAA71462.1; -.
DR EMBL; Y08756; CAA70002.1; -.
DR EMBL; Y09586; CAA70774.1; -.
DR EMBL; Y13584; CAA73911.1; -.
DR EMBL; AJ011371; CAA09600.1; -.
DR EMBL; AJ243213; CAB71316.1; -.
DR EMBL; Z48150; CAA88167.1; -.
DR GCRDb; GCR_1064; -.
DR MIM; 602164; -.
DR InterPro; IPR000276; -.
DR InterPro; IPR001520; -.
DR InterPro; IPR002233; -.
DR Pfam; PF00001; 7tm_1; 1.
DR PRINTS; PR00237; GPCRRHODOPSN.
DR PRINTS; PR01059; 5HT4RECEPTR.
DR PRINTS; PR01103; ADRENERGICR.
DR PROSITE; PS00237; G_PROTEIN_RECEP_F1_1; 1.
DR PROSITE; PS50262; G_PROTEIN_RECEP_F1_2; 1.
KW G-protein coupled receptor; Transmembrane; Glycoprotein;
KW Multigene family; Lipoprotein; Palmitate; Alternative splicing.
FT DOMAIN 1 19 EXTRACELLULAR (POTENTIAL).
FT TRANSMEM 20 40 1 (POTENTIAL).
FT DOMAIN 41 58 CYTOPLASMIC (POTENTIAL).
FT TRANSMEM 59 79 2 (POTENTIAL).
FT DOMAIN 80 93 EXTRACELLULAR (POTENTIAL).
FT TRANSMEM 94 116 3 (POTENTIAL).
FT DOMAIN 117 137 CYTOPLASMIC (POTENTIAL).
FT TRANSMEM 138 158 4 (POTENTIAL).
FT DOMAIN 159 192 EXTRACELLULAR (POTENTIAL).
FT TRANSMEM 193 213 5 (POTENTIAL).
FT DOMAIN 214 260 CYTOPLASMIC (POTENTIAL).
FT TRANSMEM 261 281 6 (POTENTIAL).
FT DOMAIN 282 294 EXTRACELLULAR (POTENTIAL).
FT TRANSMEM 295 315 7 (POTENTIAL).
FT DOMAIN 316 388 CYTOPLASMIC (POTENTIAL).
FT CARBOHYD 7 7 N-LINKED (GLCNAC...) (POTENTIAL).
FT DISULFID 93 184 BY SIMILARITY.
FT LIPID 329 329 PALMITATE (BY SIMILARITY).
FT VARSPLIC 169 169 L -> LERSLNQGLGQDFHA (IN ISOFORM 5-
FT HT4(F)).
FT VARSPLIC 359 388 RDAVECGGQWESQCHPPATSPLVAAQPSDT -> SGCSPVS
FT SFLLLFCNRPVPV (IN ISOFORM 5-HT4(E)).
FT VARSPLIC 359 388 RDAVECGGQWESQCHPPATSPLVAAQPSDT -> SSGTETD
FT RRNFGIRKRRLTKPS (IN ISOFORM 5-HT4(D)).
FT VARSPLIC 360 388 DAVECGGQWESQCHPPATSPLVAAQPSDT -> F (IN
FT ISOFORM 5-HT4(C)).
FT VARSPLIC 360 388 DAVECGGQWESQCHPPATSPLVAAQPSDT -> YTVLHRGH
FT HQELEKLPIHNDPESLESCF (IN ISOFORM 5-
FT HT4(A)).
SQ SEQUENCE 388 AA; 43761 MW; 7FCFEC60E7BDF560 CRC64;
MDKLDANVSS EEGFGSVEKV VLLTFLSTVI LMAILGNLLV MVAVCWDRQL RKIKTNYFIV
SLAFADLLVS VLVMPFGAIE LVQDIWIYGE VFCLVRTSLD VLLTTASIFH LCCISLDRYY
AICCQPLVYR NKMTPLRIAL MLGGCWVIPT FISFLPIMQG WNNIGIIDLI EKRKFNQNSN
STYCVFMVNK PYAITCSVVA FYIPFLLMVL AYYRIYVTAK EHAHQIQMLQ RAGASSESRP
QSADQHSTHR MRTETKAAKT LCIIMGCFCL CWAPFFVTNI VDPFIDYTVP GQVWTAFLWL
GYINSGLNPF LYAFLNKSFR RAFLIILCCD DERYRRPSIL GQTVPCSTTT INGSTHVLRD
AVECGGQWES QCHPPATSPL VAAQPSDT
//

250
Tests/SwissProt/sp011
View File

@ -1,250 +0,0 @@
ID LSHR_RAT STANDARD; PRT; 700 AA.
AC P16235; P70646; Q63807; Q63808; Q63809;
DT 01-APR-1990 (Rel. 14, Created)
DT 01-APR-1990 (Rel. 14, Last sequence update)
DT 01-OCT-2000 (Rel. 40, Last annotation update)
DE LUTROPIN-CHORIOGONADOTROPIC HORMONE RECEPTOR PRECURSOR (LH/CG-R)
DE (LSH-R) (LUTEINIZING HORMONE RECEPTOR).
GN LHCGR.
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP SEQUENCE FROM N.A.
RX MEDLINE=89332512; PubMed=2502842;
RA McFarland K.C., Sprengel R., Phillips H.S., Koehler M.,
RA Rosemblit N., Nikolics K., Segaloff D.L., Seeburg P.H.;
RT "Lutropin-choriogonadotropin receptor: an unusual member of the G
RT protein-coupled receptor family.";
RL Science 245:494-499(1989).
RN [2]
RP SEQUENCE FROM N.A., AND ALTERNATIVE SPLICING.
RC STRAIN=SPRAGUE-DAWLEY; TISSUE=Ovary;
RX MEDLINE=92347604; PubMed=1353463;
RA Aatsinki J.T., Pietila E.M., Lakkakorpi J.T., Rajaniemi H.J.;
RT "Expression of the LH/CG receptor gene in rat ovarian tissue is
RT regulated by an extensive alternative splicing of the primary
RT transcript.";
RL Mol. Cell. Endocrinol. 84:127-135(1992).
RN [3]
RP SEQUENCE FROM N.A.
RX MEDLINE=91209270; PubMed=2019252;
RA Koo Y.B., Slaughter R.G., Ji T.H.;
RT "Structure of the luteinizing hormone receptor gene and multiple
RT exons of the coding sequence.";
RL Endocrinology 128:2297-2308(1991).
RN [4]
RP SEQUENCE FROM N.A., AND ALTERNATIVE SPLICING.
RX MEDLINE=91006819; PubMed=1976554;
RA Bernard M.P., Myers R.V., Moyle W.R.;
RT "Cloning of rat lutropin (LH) receptor analogs lacking the soybean
RT lectin domain.";
RL Mol. Cell. Endocrinol. 71:R19-R23(1990).
RN [5]
RP SEQUENCE FROM N.A., AND ALTERNATIVE SPLICING.
RX MEDLINE=91126285; PubMed=2281186;
RA Segaloff D.L., Sprengel R., Nikolics K., Ascoli M.;
RT "Structure of the lutropin/choriogonadotropin receptor.";
RL Recent Prog. Horm. Res. 46:261-303(1990).
RN [6]
RP SEQUENCE OF 295-700 FROM N.A.
RX MEDLINE=91060531; PubMed=2174034;
RA Tsai-Morris C.H., Buczko E., Wang W., Dufau M.L.;
RT "Intronic nature of the rat luteinizing hormone receptor gene defines
RT a soluble receptor subspecies with hormone binding activity.";
RL J. Biol. Chem. 265:19385-19388(1990).
RN [7]
RP SEQUENCE OF 27-37.
RX MEDLINE=89174723; PubMed=2925659;
RA Roche P.C., Ryan R.J.;
RT "Purification, characterization, and amino-terminal sequence of rat
RT ovarian receptor for luteinizing hormone/human choriogonadotropin.";
RL J. Biol. Chem. 264:4636-4641(1989).
RN [8]
RP MUTAGENESIS.
RX MEDLINE=91332007; PubMed=1714448;
RA Ji I., Ji T.H.;
RT "Asp383 in the second transmembrane domain of the lutropin receptor
RT is important for high affinity hormone binding and cAMP production.";
RL J. Biol. Chem. 266:14953-14957(1991).
CC -!- FUNCTION: RECEPTOR FOR LUTROPIN-CHORIOGONADOTROPIC HORMONE.
CC THE ACTIVITY OF THIS RECEPTOR IS MEDIATED BY G PROTEINS WHICH
CC ACTIVATE ADENYLATE CYCLASE.
CC -!- SUBCELLULAR LOCATION: INTEGRAL MEMBRANE PROTEIN.
CC -!- ALTERNATIVE PRODUCTS: AT LEAST 11 ISOFORMS WHICH DIFFER IN
CC SUBCELLULAR LOCATION ARE PRODUCED BY ALTERNATIVE SPLICING
CC OF THE SAME GENE.
CC -!- SIMILARITY: BELONGS TO FAMILY 1 OF G-PROTEIN COUPLED RECEPTORS.
CC FSH/LSH/TSH SUBFAMILY.
CC -!- SIMILARITY: CONTAINS 7 LEUCINE-RICH REPEATS (LRR).
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; M26199; AAA41528.1; -.
DR EMBL; M61212; AAA41527.1; -.
DR EMBL; M61211; AAA41527.1; JOINED.
DR EMBL; S40803; AAB22680.1; -.
DR EMBL; S40787; AAB22680.1; JOINED.
DR EMBL; S40903; AAB22680.1; JOINED.
DR EMBL; S40904; AAB22680.1; JOINED.
DR EMBL; S40905; AAB22680.1; JOINED.
DR EMBL; S40907; AAB22680.1; JOINED.
DR EMBL; S40909; AAB22680.1; JOINED.
DR EMBL; S40918; AAB22680.1; JOINED.
DR EMBL; S40920; AAB22680.1; JOINED.
DR EMBL; S40795; AAB22680.1; JOINED.
DR EMBL; S40798; AAB22680.1; JOINED.
DR EMBL; S40795; AAB22681.1; -.
DR EMBL; S40787; AAB22681.1; JOINED.
DR EMBL; S40903; AAB22681.1; JOINED.
DR EMBL; S40904; AAB22681.1; JOINED.
DR EMBL; S40905; AAB22681.1; JOINED.
DR EMBL; S40907; AAB22681.1; JOINED.
DR EMBL; S40909; AAB22681.1; JOINED.
DR EMBL; S40918; AAB22681.1; JOINED.
DR EMBL; S40920; AAB22681.1; JOINED.
DR EMBL; S40803; AAB22682.2; -.
DR EMBL; S40787; AAB22682.2; JOINED.
DR EMBL; S40903; AAB22682.2; JOINED.
DR EMBL; S40907; AAB22682.2; JOINED.
DR EMBL; S40909; AAB22682.2; JOINED.
DR EMBL; S40918; AAB22682.2; JOINED.
DR EMBL; S40920; AAB22682.2; JOINED.
DR EMBL; S40795; AAB22682.2; JOINED.
DR EMBL; S40798; AAB22682.2; JOINED.
DR EMBL; S40803; AAB22683.1; -.
DR EMBL; S40787; AAB22683.1; JOINED.
DR EMBL; S40903; AAB22683.1; JOINED.
DR EMBL; S40904; AAB22683.1; JOINED.
DR EMBL; S40905; AAB22683.1; JOINED.
DR EMBL; S40907; AAB22683.1; JOINED.
DR EMBL; S40909; AAB22683.1; JOINED.
DR EMBL; S40918; AAB22683.1; JOINED.
DR EMBL; S40920; AAB22683.1; JOINED.
DR EMBL; S40795; AAB22683.1; JOINED.
DR EMBL; S40798; AAB22683.1; JOINED.
DR EMBL; S40803; AAB22684.2; -.
DR EMBL; S40787; AAB22684.2; JOINED.
DR EMBL; S40903; AAB22684.2; JOINED.
DR EMBL; S40904; AAB22684.2; JOINED.
DR EMBL; S40905; AAB22684.2; JOINED.
DR EMBL; S40909; AAB22684.2; JOINED.
DR EMBL; S40918; AAB22684.2; JOINED.
DR EMBL; S40920; AAB22684.2; JOINED.
DR EMBL; S40795; AAB22684.2; JOINED.
DR EMBL; S40798; AAB22684.2; JOINED.
DR EMBL; M68928; AAA41529.1; -.
DR EMBL; M68917; AAA41529.1; JOINED.
DR EMBL; M68918; AAA41529.1; JOINED.
DR EMBL; M68919; AAA41529.1; JOINED.
DR EMBL; M68920; AAA41529.1; JOINED.
DR EMBL; M68921; AAA41529.1; JOINED.
DR EMBL; M68922; AAA41529.1; JOINED.
DR EMBL; M68923; AAA41529.1; JOINED.
DR EMBL; M68925; AAA41529.1; JOINED.
DR EMBL; M68926; AAA41529.1; JOINED.
DR EMBL; M68927; AAA41529.1; JOINED.
DR PIR; A32460; A32460.
DR PIR; A41343; A41343.
DR HSSP; P22888; 1LUT.
DR GCRDb; GCR_0138; -.
DR GCRDb; GCR_0139; -.
DR GCRDb; GCR_0262; -.
DR GCRDb; GCR_0612; -.
DR GCRDb; GCR_0613; -.
DR GCRDb; GCR_0614; -.
DR InterPro; IPR000276; -.
DR InterPro; IPR001611; -.
DR InterPro; IPR002131; -.
DR InterPro; IPR002273; -.
DR Pfam; PF00001; 7tm_1; 1.
DR Pfam; PF00560; LRR; 2.
DR PRINTS; PR00373; GLYCHORMONER.
DR PRINTS; PR01144; LSHRECEPTOR.
DR PROSITE; PS00237; G_PROTEIN_RECEP_F1_1; 1.
DR PROSITE; PS50262; G_PROTEIN_RECEP_F1_2; 1.
KW G-protein coupled receptor; Transmembrane; Glycoprotein; Signal;
KW Phosphorylation; Repeat; Leucine-rich repeat; Alternative splicing.
FT SIGNAL 1 26
FT CHAIN 27 700 LUTROPIN-CHORIOGONADOTROPIC HORMONE
FT RECEPTOR.
FT DOMAIN 27 362 EXTRACELLULAR (POTENTIAL).
FT TRANSMEM 363 390 1 (POTENTIAL).
FT DOMAIN 391 399 CYTOPLASMIC (POTENTIAL).
FT TRANSMEM 400 422 2 (POTENTIAL).
FT DOMAIN 423 443 EXTRACELLULAR (POTENTIAL).
FT TRANSMEM 444 466 3 (POTENTIAL).
FT DOMAIN 467 486 CYTOPLASMIC (POTENTIAL).
FT TRANSMEM 487 509 4 (POTENTIAL).
FT DOMAIN 510 529 EXTRACELLULAR (POTENTIAL).
FT TRANSMEM 530 551 5 (POTENTIAL).
FT DOMAIN 552 574 CYTOPLASMIC (POTENTIAL).
FT TRANSMEM 575 598 6 (POTENTIAL).
FT DOMAIN 599 609 EXTRACELLULAR (POTENTIAL).
FT TRANSMEM 610 631 7 (POTENTIAL).
FT DOMAIN 632 700 CYTOPLASMIC (POTENTIAL).
FT REPEAT 52 75 LRR 1.
FT REPEAT 126 150 LRR 2.
FT REPEAT 152 175 LRR 3.
FT REPEAT 176 200 LRR 4.
FT REPEAT 202 224 LRR 5.
FT REPEAT 225 248 LRR 6.
FT REPEAT 250 271 LRR 7.
FT DISULFID 443 518 BY SIMILARITY.
FT CARBOHYD 103 103 N-LINKED (GLCNAC...) (POTENTIAL).
FT CARBOHYD 178 178 N-LINKED (GLCNAC...) (POTENTIAL).
FT CARBOHYD 199 199 N-LINKED (GLCNAC...) (POTENTIAL).
FT CARBOHYD 295 295 N-LINKED (GLCNAC...) (POTENTIAL).
FT CARBOHYD 303 303 N-LINKED (GLCNAC...) (POTENTIAL).
FT CARBOHYD 317 317 N-LINKED (GLCNAC...) (POTENTIAL).
FT VARSPLIC 83 132 MISSING (IN ISOFORM 1950).
FT VARSPLIC 133 157 MISSING (IN ISOFORM 1759).
FT VARSPLIC 184 700 MISSING (IN ISOFORM C2).
FT VARSPLIC 232 251 DISSTKLQALPSHGLESIQT -> PCRATGWSPFRRSSPC
FT LPTH (IN ISOFORM 2075).
FT VARSPLIC 232 293 MISSING (IN ISOFORM E/A2, ISOFORM EB AND
FT ISOFORM B1).
FT VARSPLIC 252 700 MISSING (IN ISOFORM 2075).
FT VARSPLIC 294 367 QNFSFSIFENFSKQCESTVRKADNETLYSAIFEENELSGW
FT DYDYGFCSPKTLQCAPEPDAFNPCEDIMGYAFLR ->
FT IFHFPFLKTSPNNAKAQLEKQITRRFIPPSLRRMNSVAGI
FT MIMASVHPRHSNVLQNQMLSTPVKILWAMPSLGS (IN
FT ISOFORM B1 AND ISOFORM B3).
FT VARSPLIC 294 294 Q -> P (IN ISOFORM C1).
FT VARSPLIC 295 700 MISSING (IN ISOFORM C1).
FT VARSPLIC 321 342 YSAIFEENELSGWDYDYGFCSP -> LHGALPAAHCLRGLP
FT NKRPVL (IN ISOFORM 1834, ISOFORM 1759 AND
FT ISOFORM EB).
FT VARSPLIC 343 700 MISSING (IN ISOFORMS 1834, ISOFORM 1759
FT AND ISOFORM EB).
FT VARSPLIC 368 700 MISSING (IN ISOFORM B1 AND ISOFORM B3).
FT VARIANT 82 82 I -> M (IN ISOFORM 1950).
FT VARIANT 179 179 E -> G (IN ISOFORM 1759).
FT VARIANT 233 233 I -> T (IN ISOFORM 1950).
FT VARIANT 646 646 G -> S (IN ISOFORM 1950).
FT MUTAGEN 409 409 D->N: SIGNIFICANT REDUCTION OF BINDING.
FT MUTAGEN 436 436 D->N: NO CHANGE IN BINDING OR CAMP PROD.
FT MUTAGEN 455 455 E->Q: NO CHANGE IN BINDING OR CAMP PROD.
FT MUTAGEN 582 582 D->N: NO CHANGE IN BINDING OR CAMP PROD.
FT CONFLICT 33 33 R -> L (IN REF. 7).
SQ SEQUENCE 700 AA; 78035 MW; 31807E73BAC94F1F CRC64;
MGRRVPALRQ LLVLAVLLLK PSQLQSRELS GSRCPEPCDC APDGALRCPG PRAGLARLSL
TYLPVKVIPS QAFRGLNEVV KIEISQSDSL ERIEANAFDN LLNLSELLIQ NTKNLLYIEP
GAFTNLPRLK YLSICNTGIR TLPDVTKISS SEFNFILEIC DNLHITTIPG NAFQGMNNES
VTLKLYGNGF EEVQSHAFNG TTLISLELKE NIYLEKMHSG AFQGATGPSI LDISSTKLQA
LPSHGLESIQ TLIALSSYSL KTLPSKEKFT SLLVATLTYP SHCCAFRNLP KKEQNFSFSI
FENFSKQCES TVRKADNETL YSAIFEENEL SGWDYDYGFC SPKTLQCAPE PDAFNPCEDI
MGYAFLRVLI WLINILAIFG NLTVLFVLLT SRYKLTVPRF LMCNLSFADF CMGLYLLLIA
SVDSQTKGQY YNHAIDWQTG SGCGAAGFFT VFASELSVYT LTVITLERWH TITYAVQLDQ
KLRLRHAIPI MLGGWLFSTL IATMPLVGIS NYMKVSICLP MDVESTLSQV YILSILILNV
VAFVVICACY IRIYFAVQNP ELTAPNKDTK IAKKMAILIF TDFTCMAPIS FFAISAAFKV
PLITVTNSKI LLVLFYPVNS CANPFLYAIF TKAFQRDFLL LLSRFGCCKR RAELYRRKEF
SAYTSNCKNG FPGASKPSQA TLKLSTVHCQ QPIPPRALTH
//

20
Tests/common_BioSQL.py
View File

@ -1450,17 +1450,17 @@ class AutoSeqIOTests(SeqRecordTestBaseClass):
self.check("fasta", "GFF/NC_001802.fna")
self.check("fasta", "GFF/multi.fna", 3)
self.check("fasta", "Registry/seqs.fasta", 2)
self.check("swiss", "SwissProt/sp001")
self.check("swiss", "SwissProt/sp002")
self.check("swiss", "SwissProt/sp003")
self.check("swiss", "SwissProt/Q13454.txt")
self.check("swiss", "SwissProt/P60904.txt")
self.check("swiss", "SwissProt/P62258.txt")
self.check("swiss", "SwissProt/P0A186.txt")
self.check("swiss", "SwissProt/sp005")
self.check("swiss", "SwissProt/sp006")
self.check("swiss", "SwissProt/sp007")
self.check("swiss", "SwissProt/sp008")
self.check("swiss", "SwissProt/sp009")
self.check("swiss", "SwissProt/sp010")
self.check("swiss", "SwissProt/sp011")
self.check("swiss", "SwissProt/P68308.txt")
self.check("swiss", "SwissProt/P39896.txt")
self.check("swiss", "SwissProt/O95832.txt")
self.check("swiss", "SwissProt/P04439.txt")
self.check("swiss", "SwissProt/O23729.txt")
self.check("swiss", "SwissProt/Q13639.txt")
self.check("swiss", "SwissProt/P16235.txt")
self.check("swiss", "SwissProt/sp012")
self.check("swiss", "SwissProt/sp013")
self.check("swiss", "SwissProt/P60137.txt")

2
Tests/seq_tests_common.py
View File

@ -227,7 +227,7 @@ class SeqRecordTestBaseClass(unittest.TestCase):
)
missing_keys = set(old.annotations).difference(new.annotations)
missing_keys = missing_keys.difference(
["ncbi_taxid", "structured_comment"] # Can't store chimeras
["gene_name", "ncbi_taxid", "structured_comment"] # Can't store chimeras
)
self.assertEqual(
len(missing_keys),

110
Tests/test_SeqIO.py
View File

@ -1898,7 +1898,7 @@ class TestSeqIO(SeqIOTestBaseClass):
def test_swiss1(self):
sequences = ["MGARGAPSRRRQAGRRLRYLPTGSFPFLLLLLLLCIQLGG...YSDLDFE"]
ids = ["Q13454"]
names = ["N33_HUMAN"]
names = ["TUSC3_HUMAN"]
lengths = [348]
alignment = None
messages = {
@ -1913,7 +1913,7 @@ class TestSeqIO(SeqIOTestBaseClass):
self.perform_test(
"swiss",
False,
"SwissProt/sp001",
"SwissProt/Q13454.txt",
1,
ids,
names,
@ -1925,23 +1925,23 @@ class TestSeqIO(SeqIOTestBaseClass):
def test_swiss2(self):
sequences = ["MADQRQRSLSTSGESLYHVLGLDKNATSDDIKKSYRKLAL...YHTDGFN"]
ids = ["P54101"]
names = ["CSP_MOUSE"]
ids = ["P60904"]
names = ["DNJC5_MOUSE"]
lengths = [198]
alignment = None
messages = {
"fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=P54101).",
"fastq-illumina": "No suitable quality scores found in letter_annotations of SeqRecord (id=P54101).",
"fastq-solexa": "No suitable quality scores found in letter_annotations of SeqRecord (id=P54101).",
"fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=P60904).",
"fastq-illumina": "No suitable quality scores found in letter_annotations of SeqRecord (id=P60904).",
"fastq-solexa": "No suitable quality scores found in letter_annotations of SeqRecord (id=P60904).",
"nib": "Sequence should contain A,C,G,T,N,a,c,g,t,n only",
"phd": "No suitable quality scores found in letter_annotations of SeqRecord (id=P54101).",
"qual": "No suitable quality scores found in letter_annotations of SeqRecord (id=P54101).",
"phd": "No suitable quality scores found in letter_annotations of SeqRecord (id=P60904).",
"qual": "No suitable quality scores found in letter_annotations of SeqRecord (id=P60904).",
"sff": "Missing SFF flow information",
}
self.perform_test(
"swiss",
False,
"SwissProt/sp002",
"SwissProt/P60904.txt",
1,
ids,
names,
@ -1953,23 +1953,23 @@ class TestSeqIO(SeqIOTestBaseClass):
def test_swiss3(self):
sequences = ["MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVE...DVEDENQ"]
ids = ["P42655"]
names = ["143E_HUMAN"]
ids = ["P62258"]
names = ["1433E_HUMAN"]
lengths = [255]
alignment = None
messages = {
"fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=P42655).",
"fastq-illumina": "No suitable quality scores found in letter_annotations of SeqRecord (id=P42655).",
"fastq-solexa": "No suitable quality scores found in letter_annotations of SeqRecord (id=P42655).",
"fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=P62258).",
"fastq-illumina": "No suitable quality scores found in letter_annotations of SeqRecord (id=P62258).",
"fastq-solexa": "No suitable quality scores found in letter_annotations of SeqRecord (id=P62258).",
"nib": "Sequence should contain A,C,G,T,N,a,c,g,t,n only",
"phd": "No suitable quality scores found in letter_annotations of SeqRecord (id=P42655).",
"qual": "No suitable quality scores found in letter_annotations of SeqRecord (id=P42655).",
"phd": "No suitable quality scores found in letter_annotations of SeqRecord (id=P62258).",
"qual": "No suitable quality scores found in letter_annotations of SeqRecord (id=P62258).",
"sff": "Missing SFF flow information",
}
self.perform_test(
"swiss",
False,
"SwissProt/sp003",
"SwissProt/P62258.txt",
1,
ids,
names,
@ -2009,23 +2009,23 @@ class TestSeqIO(SeqIOTestBaseClass):
def test_swiss5(self):
sequences = ["MNLLLTLLTNTTLALLLVFIAFWLPQLNVYAEKTSPYECG...EGLEWAE"]
ids = ["P24973"]
ids = ["P68308"]
names = ["NU3M_BALPH"]
lengths = [115]
alignment = None
messages = {
"fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=P24973).",
"fastq-illumina": "No suitable quality scores found in letter_annotations of SeqRecord (id=P24973).",
"fastq-solexa": "No suitable quality scores found in letter_annotations of SeqRecord (id=P24973).",
"fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=P68308).",
"fastq-illumina": "No suitable quality scores found in letter_annotations of SeqRecord (id=P68308).",
"fastq-solexa": "No suitable quality scores found in letter_annotations of SeqRecord (id=P68308).",
"nib": "Sequence should contain A,C,G,T,N,a,c,g,t,n only",
"phd": "No suitable quality scores found in letter_annotations of SeqRecord (id=P24973).",
"qual": "No suitable quality scores found in letter_annotations of SeqRecord (id=P24973).",
"phd": "No suitable quality scores found in letter_annotations of SeqRecord (id=P68308).",
"qual": "No suitable quality scores found in letter_annotations of SeqRecord (id=P68308).",
"sff": "Missing SFF flow information",
}
self.perform_test(
"swiss",
False,
"SwissProt/sp005",
"SwissProt/P68308.txt",
1,
ids,
names,
@ -2053,7 +2053,7 @@ class TestSeqIO(SeqIOTestBaseClass):
self.perform_test(
"swiss",
False,
"SwissProt/sp006",
"SwissProt/P39896.txt",
1,
ids,
names,
@ -2081,7 +2081,7 @@ class TestSeqIO(SeqIOTestBaseClass):
self.perform_test(
"swiss",
False,
"SwissProt/sp007",
"SwissProt/O95832.txt",
1,
ids,
names,
@ -2092,24 +2092,24 @@ class TestSeqIO(SeqIOTestBaseClass):
)
def test_swiss8(self):
sequences = ["MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFFTSVSRPG...SLTACKV"]
ids = ["P01892"]
names = ["1A02_HUMAN"]
sequences = ["MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPG...SLTACKV"]
ids = ["P04439"]
names = ["HLAA_HUMAN"]
lengths = [365]
alignment = None
messages = {
"fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=P01892).",
"fastq-illumina": "No suitable quality scores found in letter_annotations of SeqRecord (id=P01892).",
"fastq-solexa": "No suitable quality scores found in letter_annotations of SeqRecord (id=P01892).",
"fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=P04439).",
"fastq-illumina": "No suitable quality scores found in letter_annotations of SeqRecord (id=P04439).",
"fastq-solexa": "No suitable quality scores found in letter_annotations of SeqRecord (id=P04439).",
"nib": "Sequence should contain A,C,G,T,N,a,c,g,t,n only",
"phd": "No suitable quality scores found in letter_annotations of SeqRecord (id=P01892).",
"qual": "No suitable quality scores found in letter_annotations of SeqRecord (id=P01892).",
"phd": "No suitable quality scores found in letter_annotations of SeqRecord (id=P04439).",
"qual": "No suitable quality scores found in letter_annotations of SeqRecord (id=P04439).",
"sff": "Missing SFF flow information",
}
self.perform_test(
"swiss",
False,
"SwissProt/sp008",
"SwissProt/P04439.txt",
1,
ids,
names,
@ -2137,35 +2137,7 @@ class TestSeqIO(SeqIOTestBaseClass):
self.perform_test(
"swiss",
False,
"SwissProt/sp009",
1,
ids,
names,
sequences,
lengths,
alignment,
messages,
)
def test_swiss10(self):
sequences = ["MDKLDANVSSEEGFGSVEKVVLLTFLSTVILMAILGNLLV...AAQPSDT"]
ids = ["Q13639"]
names = ["5H4_HUMAN"]
lengths = [388]
alignment = None
messages = {
"fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).",
"fastq-illumina": "No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).",
"fastq-solexa": "No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).",
"nib": "Sequence should contain A,C,G,T,N,a,c,g,t,n only",
"phd": "No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).",
"qual": "No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).",
"sff": "Missing SFF flow information",
}
self.perform_test(
"swiss",
False,
"SwissProt/sp010",
"SwissProt/O23729.txt",
1,
ids,
names,
@ -2193,7 +2165,7 @@ class TestSeqIO(SeqIOTestBaseClass):
self.perform_test(
"swiss",
False,
"SwissProt/sp011",
"SwissProt/P16235.txt",
1,
ids,
names,
@ -2345,10 +2317,10 @@ class TestSeqIO(SeqIOTestBaseClass):
)
def test_swiss17(self):
sequences = ["ARRERMTAREEASLRTLEGRRRATLLSARQGMMSARGDFL...TKNFGFV"]
sequences = ["MNKQAVKRLHMLREVSEKLNKYNLNSHPPLNVLEQATIKQ...TKNFGFV"]
ids = ["Q62671"]
names = ["EDD_RAT"]
lengths = [920]
names = ["UBR5_RAT"]
lengths = [2788]
alignment = None
messages = {
"fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=Q62671).",

4
Tests/test_SeqIO_index.py
View File

@ -373,8 +373,8 @@ class IndexDictTests(SeqRecordTestBaseClass, SeqIOTestBaseClass):
("NBRF/B_nuc.pir", "pir"),
("NBRF/Cw_prot.pir", "pir"),
("NBRF/clustalw.pir", "pir"),
("SwissProt/sp001", "swiss"),
("SwissProt/sp010", "swiss"),
("SwissProt/Q13454.txt", "swiss"),
("SwissProt/Q13639.txt", "swiss"),
("SwissProt/sp016", "swiss"),
("SwissProt/multi_ex.txt", "swiss"),
("SwissProt/multi_ex.xml", "uniprot-xml"),

5915
Tests/test_SwissProt.py
View File

File diff suppressed because it is too large Load Diff

13
Tests/test_Uniprot.py
View File

@ -473,9 +473,9 @@ class TestUniprot(SeqRecordTestBaseClass):
# test Entry version
self.assertEqual(seq_record.annotations["entry_version"], 93)
def test_sp002(self):
"""Parsing SwissProt file sp002."""
filename = "sp002"
def test_P60904(self):
"""Parsing SwissProt file P60904.txt."""
filename = "P60904.txt"
# test the record parser
datafile = os.path.join("SwissProt", filename)
@ -486,9 +486,9 @@ class TestUniprot(SeqRecordTestBaseClass):
self.assertIsInstance(seq_record, SeqRecord)
# test Sequence version
self.assertEqual(seq_record.annotations["sequence_version"], 34)
self.assertEqual(seq_record.annotations["sequence_version"], 1)
# test Entry version
self.assertEqual(seq_record.annotations["entry_version"], 36)
self.assertEqual(seq_record.annotations["entry_version"], 158)
def compare_txt_xml(self, old, new):
"""Compare text and XML based parser output."""
@ -565,7 +565,8 @@ class TestUniprot(SeqRecordTestBaseClass):
# TODO - Why the mismatch gene_name vs gene_name_primary?
# TODO - Handle evidence codes on GN line (see GitHub isse #416)
self.assertEqual(
old.annotations["gene_name"], "Name=HvPIP2;8 {ECO:0000313|EMBL:BAN04711.1};"
old.annotations["gene_name"],
[{"Name": "HvPIP2;8 {ECO:0000313|EMBL:BAN04711.1}"}],
)
self.assertEqual(new.annotations["gene_name_primary"], "HvPIP2;8")
self.assertEqual(old.name, "F2CXE6_HORVD")