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# 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
//
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