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Resolved problem with db_xref in GenBank/protein_refseq.gb, the NCBI have replaced an 'odd' entry - thus the additional test GenBank file for NP_034640
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peterc
153
Tests/GenBank/protein_refseq2.gb
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153
Tests/GenBank/protein_refseq2.gb
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LOCUS NP_034640 182 aa linear ROD 15-NOV-2007
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DEFINITION interferon beta 1, fibroblast precursor [Mus musculus].
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ACCESSION NP_034640
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VERSION NP_034640.1 GI:6754304
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DBSOURCE REFSEQ: accession NM_010510.1
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KEYWORDS .
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SOURCE Mus musculus (house mouse)
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ORGANISM Mus musculus
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Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
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Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
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Sciurognathi; Muroidea; Muridae; Murinae; Mus.
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REFERENCE 1 (residues 1 to 182)
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AUTHORS Schroder,K., Spille,M., Pilz,A., Lattin,J., Bode,K.A., Irvine,K.M.,
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Burrows,A.D., Ravasi,T., Weighardt,H., Stacey,K.J., Decker,T.,
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Hume,D.A., Dalpke,A.H. and Sweet,M.J.
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TITLE Differential effects of CpG DNA on IFN-beta induction and STAT1
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activation in murine macrophages versus dendritic cells:
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alternatively activated STAT1 negatively regulates TLR signaling in
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macrophages
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JOURNAL J. Immunol. 179 (6), 3495-3503 (2007)
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PUBMED 17785783
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REMARK GeneRIF: The interferon-beta/STAT1 axis is a key regulator of CpG
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DNA signaling; divergent activation of this pathway between bone
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marrow-derived macrophages and myeloid dendritic cells dictates
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cell-specific immune responses.
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REFERENCE 2 (residues 1 to 182)
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AUTHORS Wang,Y.X., da Cunha,V., Vincelette,J., White,K., Velichko,S.,
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Xu,Y., Gross,C., Fitch,R.M., Halks-Miller,M., Larsen,B.R.,
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Yajima,T., Knowlton,K.U., Vergona,R., Sullivan,M.E. and Croze,E.
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TITLE Antiviral and myocyte protective effects of murine interferon-beta
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and -{alpha}2 in coxsackievirus B3-induced myocarditis and
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epicarditis in Balb/c mice
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JOURNAL Am. J. Physiol. Heart Circ. Physiol. 293 (1), H69-H76 (2007)
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PUBMED 17434974
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REMARK GeneRIF: These data demonstrate antiviral effects for both
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mIFN-beta and mIFN-alpha(2), which lead to protection of the mice
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from CVB3-induced myocarditis.
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REFERENCE 3 (residues 1 to 182)
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AUTHORS Chang,E.Y., Guo,B., Doyle,S.E. and Cheng,G.
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TITLE Cutting edge: involvement of the type I IFN production and
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signaling pathway in lipopolysaccharide-induced IL-10 production
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JOURNAL J. Immunol. 178 (11), 6705-6709 (2007)
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PUBMED 17513714
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REMARK GeneRIF: Type I interferon production and signaling pathway play a
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role in regulating the lipopolysaccharide response in bone
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marrow-derived macrophages.
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REFERENCE 4 (residues 1 to 182)
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AUTHORS Meissner,N., Rutkowski,M., Harmsen,A.L., Han,S. and Harmsen,A.G.
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TITLE Type I interferon signaling and B cells maintain hemopoiesis during
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Pneumocystis infection of the lung
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JOURNAL J. Immunol. 178 (10), 6604-6615 (2007)
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PUBMED 17475892
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REMARK GeneRIF: Both interferon-beta and -alpha genes are required in the
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regenerative capabilities of the hemopoietic system under the
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pressure of Pneumocystis infection.
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REFERENCE 5 (residues 1 to 182)
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AUTHORS Henry,T., Brotcke,A., Weiss,D.S., Thompson,L.J. and Monack,D.M.
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TITLE Type I interferon signaling is required for activation of the
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inflammasome during Francisella infection
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JOURNAL J. Exp. Med. 204 (5), 987-994 (2007)
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PUBMED 17452523
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REFERENCE 6 (residues 1 to 182)
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AUTHORS Senda,T., Shimazu,T., Matsuda,S., Kawano,G., Shimizu,H.,
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Nakamura,K.T. and Mitsui,Y.
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TITLE Three-dimensional crystal structure of recombinant murine
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interferon-beta
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JOURNAL EMBO J. 11 (9), 3193-3201 (1992)
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PUBMED 1505514
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REFERENCE 7 (residues 1 to 182)
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AUTHORS Cornall,R.J., Friedman,J.M. and Todd,J.A.
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TITLE Mouse microsatellites from a flow-sorted 4:6 Robertsonian
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chromosome
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JOURNAL Mamm. Genome 3 (11), 620-624 (1992)
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PUBMED 1450512
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REFERENCE 8 (residues 1 to 182)
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AUTHORS Tanaka,N. and Taniguchi,T.
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TITLE Cytokine gene regulation: regulatory cis-elements and DNA binding
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factors involved in the interferon system
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JOURNAL Adv. Immunol. 52, 263-281 (1992)
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PUBMED 1442307
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REMARK Review article
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REFERENCE 9 (residues 1 to 182)
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AUTHORS Le Roy,H., Simon-Chazottes,D., Montagutelli,X. and Guenet,J.L.
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TITLE A set of anonymous DNA clones as markers for mouse gene mapping
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JOURNAL Mamm. Genome 3 (4), 244-246 (1992)
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PUBMED 1351769
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REFERENCE 10 (residues 1 to 182)
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AUTHORS Levan,G., Szpirer,J., Szpirer,C., Klinga,K., Hanson,C. and
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Islam,M.Q.
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TITLE The gene map of the Norway rat (Rattus norvegicus) and comparative
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mapping with mouse and man
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JOURNAL Genomics 10 (3), 699-718 (1991)
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PUBMED 1889815
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COMMENT VALIDATED REFSEQ: This record has undergone preliminary review of
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the sequence, but has not yet been subject to final review. The
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reference sequence was derived from K00020.1.
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Publication Note: This RefSeq record includes a subset of the
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publications that are available for this gene. Please see the
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Entrez Gene record to access additional publications.
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FEATURES Location/Qualifiers
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source 1..182
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/organism="Mus musculus"
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/db_xref="taxon:10090"
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/chromosome="4"
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/map="4 42.6 cM"
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Protein 1..182
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/product="interferon beta 1, fibroblast precursor"
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sig_peptide 1..21
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/note="ifn-beta"
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/calculated_mol_wt=2410
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mat_peptide 22..182
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/product="ifn-beta"
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/calculated_mol_wt=19735
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Region 27..173
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/region_name="IFab"
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/note="Interferon alpha, beta. Includes also interferon
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omega and tau. Different from interferon gamma family;
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cd00095"
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/db_xref="CDD:28979"
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Site order(29..30,33,36..37,40,43..44,96..97,99..100,102..103,
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106,109..110,113..114,117)
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/site_type="other"
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/note="putative IFNAR-1 binding site"
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/db_xref="CDD:28979"
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Site order(51..58,60..62,66..67,136..137,139..140,143..144,
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146..147,150..155)
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/site_type="other"
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/note="putative IFNAR-2 binding site"
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/db_xref="CDD:28979"
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Site 97
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/site_type="other"
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/note="N-glycosylation site"
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/db_xref="CDD:28979"
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CDS 1..182
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/gene="Ifnb1"
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/coded_by="NM_010510.1:21..569"
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/GO_component="extracellular region"
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/GO_function="cytokine activity;
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hematopoietin/interferon-class (D200-domain) cytokine
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receptor binding"
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/GO_process="defense response; defense response to
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bacterium; response to virus"
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/db_xref="CCDS:CCDS18318.1"
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/db_xref="GeneID:15977"
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/db_xref="MGI:107657"
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ORIGIN
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1 mnnrwilhaa fllcfsttal sinykqlqlq ertnirkcqe lleqlngkin ltyradfkip
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61 memtekmqks ytafaiqeml qnvflvfrnn fsstgwneti vvrlldelhq qtvflktvle
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121 ekqeerltwe msstalhlks yywrvqrylk lmkynsyawm vvraeifrnf liirrltrnf
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181 qn
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//
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@ -123,7 +123,7 @@ Testing loading from genbank format file GenBank/arab1.gb
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- Retrieving by version 'AC007323.5', OK
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- Retrieving by accession 'AC007323', OK
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- Retrieving by GI '6587720', OK
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Testing loading from genbank format file GenBank/protein_refseq.gb
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Testing loading from genbank format file GenBank/protein_refseq2.gb
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- MNNRWILHAAFLLCFSTTA...FQN [+/OSLiyGWcFWiLWgW/xDKe+6Ml8] len 182, NP_034640.1
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- Retrieving by name/display_id 'NP_034640', OK
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- Retrieving by version 'NP_034640.1', OK
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@ -59,7 +59,9 @@ test_files = [ \
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("genbank",False, 'GenBank/iro.gb', 1),
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("genbank",False, 'GenBank/pri1.gb', 1),
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("genbank",False, 'GenBank/arab1.gb', 1),
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("genbank",False, 'GenBank/protein_refseq.gb', 1),
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#protein_refseq.gb had malformed db_xref, fixed in protein_refseq2.gb
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#("genbank",False, 'GenBank/protein_refseq.gb', 1),
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("genbank",False, 'GenBank/protein_refseq2.gb', 1),
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("genbank",False, 'GenBank/extra_keywords.gb', 1),
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("genbank",False, 'GenBank/one_of.gb', 1),
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("genbank",False, 'GenBank/NT_019265.gb', 1),
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@ -115,6 +117,9 @@ def compare_records(old, new) :
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assert Set(old_f.qualifiers.keys()) == Set(new_f.qualifiers.keys())
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for key in old_f.qualifiers.keys() :
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if key == "db_xref":
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#Should be a list
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assert Set(old_f.qualifiers[key]) == Set(new_f.qualifiers[key]), \
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"db_xref:\n%s\n%s" % (old_f.qualifiers[key], new_f.qualifiers[key])
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pass #TODO - Fix this, e.g. file GenBank/protein_refseq.gb
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else :
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assert old_f.qualifiers[key] == new_f.qualifiers[key]
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