# STOCKHOLM 1.0

#=GF AC   RF00511
#=GF ID   IRES_KSHV
#=GF DE   Kaposi's sarcoma-associated herpesvirus internal ribosome entry site
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Published; 11160685, INFERNAL
#=GF SS   Published; PMID:11160685
#=GF GA   100.00
#=GF TC   317.10
#=GF NC   30.10
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   11160685
#=GF RT   Kaposi's sarcoma-associated herpesvirus vCyclin open reading frame
#=GF RT   contains an internal ribosome entry site.
#=GF RA   Bieleski L, Talbot SJ
#=GF RL   J Virol 2001;75:1864-1869.
#=GF RN   [2]
#=GF RM   14993645
#=GF RT   A polypyrimidine tract facilitates the expression of Kaposi's
#=GF RT   sarcoma-associated herpesvirus vFLIP through an internal ribosome entry
#=GF RT   site.
#=GF RA   Bieleski L, Hindley C, Talbot SJ
#=GF RL   J Gen Virol 2004;85:615-620.
#=GF CC   This family represents the Kaposi's sarcoma-associated herpesvirus (KSHV)
#=GF CC   internal ribosome entry site (IRES) present in the vCyclin gene. The
#=GF CC   vCyclin and vFLIP coding sequences are present on a bicistronic transcript
#=GF CC   and it is thought the IRES may initiate translation of vFLIP from this
#=GF CC   bicistronic transcript [1,2].
#=GF WK   Kaposi's_sarcoma-associated_herpesvirus_internal_ribosome_entry_site_/
#=GF WK   (IRES)
#=GF SQ   5


AF148805.2/123462-123215 UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG
U40667.1/2005-2252       UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGGUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGGUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG
U79416.1/354-601         UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUAACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCGACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG
U93872.2/123729-123482   UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUAACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG
U75698.1/123214-122967   UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG
#=GC SS_cons             :::::::::<<<---<<<<<<<<<<---<<<<<--<<<<<-------<<<<<______>>>>>---->>>>>---->>>>>--->>>>>->>>>>-->>>,,<<<_______>>>-----------------((((((((((,,,<<<<----<<-<<<<<<------<<-<<<____>>>->>---->>>>>>>>--->>>>,,,,,,,,,,,<<<_____>>>,))))))-----)))):::::::
#=GC RF                  UUGCUAUGCCGCGGCaGaCuCCucuUCCCGCCaAGaaCuuAUAGACCaGGaGAAAGAACuCCuUGAGaaGuuGGCGuGGCGAACagaGGCaGuCuUAGCGACGGaCGUaACUuCCUUCUUGUUACUUAAAUUGcuGgGgGGCUCCCaaCACCUGGACuuuuGGCACCACgAGGuCaACaCCCcGAUUACaaaaGCCUUAGuuGACCCAAAGACUGGcUCAUUgCCCGCCcCcAUUAUCagCGCUGCAG
//
