# STOCKHOLM 1.0
#=GF ID Sarbecovirus-5UTR
#=GF AC RF03120
#=GF DE Sarbecovirus 5'UTR
#=GF AU Lamkiewicz K; 0000-0002-6375-6441
#=GF GA 150.0
#=GF NC 74.5
#=GF TC 229.1
#=GF PI SARS-CoV-2-5UTR;
#=GF SE Lamkiewicz K
#=GF SS Predicted;
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 50.00 -Z 2958934 CM SEQDB
#=GF CL CL00116
#=GF DR GO; 0039694; viral RNA genome replication;
#=GF DR SO; 0001201; positive_sense_ssRNA_viral_sequence;
#=GF DR SO; 0000837; UTR_region;
#=GF RN [1]
#=GF RM 15220462
#=GF RT The 3' cis-acting genomic replication element of the severe acute
#=GF RT respiratory syndrome coronavirus can function in the murine coronavirus
#=GF RT genome.
#=GF RA Goebel SJ, Taylor J, Masters PS
#=GF RL J Virol. 2004;78:7846-7851.
#=GF RN [2]
#=GF RM 25736566
#=GF RT The structure and functions of coronavirus genomic 3' and 5' ends.
#=GF RA Yang D, Leibowitz JL
#=GF RL Virus Res. 2015;206:120-133.
#=GF RN [3]
#=GF RM 21378501
#=GF RT RNA-RNA and RNA-protein interactions in coronavirus replication and
#=GF RT transcription.
#=GF RA Sola I, Mateos-Gomez PA, Almazan F, Zuniga S, Enjuanes L
#=GF RL RNA Biol. 2011;8:237-248.
#=GF RN [4]
#=GF RM 27712622
#=GF RT Coronavirus cis-Acting RNA Elements.
#=GF RA Madhugiri R, Fricke M, Marz M, Ziebuhr J
#=GF RL Adv Virus Res. 2016;96:127-163.
#=GF RN [5]
#=GF RM 35236777
#=GF RT Correlated sequence signatures are present within the genomic 5'UTR RNA
#=GF RT and NSP1 protein in coronaviruses.
#=GF RA Sosnowski P, Tidu A, Eriani G, Westhof E, Martin F
#=GF RL RNA. 2022;28:729-741.
#=GF CC The 5' UTR of Sarbecovirus consists of 4 distinct stem-loops, namely SL1,
#=GF CC SL2, SL3 and SL4. Further, there is a larger structure, SL5, present,
#=GF CC which includes the first ORFs of the polyprotein. Note, that SL3 is
#=GF CC typically present in SARS coronaviruses, but not necessarily conserved
#=GF CC among other betacoronaviruses. SL1 is important for viral replication,
#=GF CC most likely playing a role in the template-switch of viral subgenomic RNA
#=GF CC transcription. SL2 is crucial for viral viability, however, the nucleotide
#=GF CC sequence can be mutated and some residues, as long as the structure
#=GF CC remains stable. SL4 is hypothesized to play a role in directing subgenomic
#=GF CC RNA synthesis during viral replication.
#=GF WK Coronavirus_5'_UTR
#=GF SQ 19

KU973692.1/1-298 AUAUUAGGUUUUUACCUACCCAGGAA--AAGCCAACCAA-CCUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUAGCUGUCGCUCGGCUGCAUGCCUAGUGCACCUACGCAGUAUAAACAAUAAUAAACUUUACUGUCGUUGACAAGAAACGAGUAACUCGUCCCUCUUCUGCAGACU
DQ071615.1/1-298 AUAUUAGGUUUUUACCUACCCAGGAA--AAGCCAACCAA-CCUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUAGCUGUCGCUUGGCUGCAUGCCUAGUGCACCUACGCAGUAUAAACAAUAAUAAACUCUACUGUCGUUGACAAGAAACGAGUAACUCGUCCCUCUUCUGCAGACU
KF367457.1/1-298 AUAUUAGGUUUUUACCUACCCAGGAA--AAGCCAACCAA-CCCCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUAGCUGUCGCUCGGCUGCAUGCCUAGUGCACCUACGCAGUAUAAACAAUAAUAAAUUUUACUGUCGUUGACAAGAAACGAGUAACUCGUCCCUCUUCUGCAGACU
MK211377.1/1-296 --UUUAGGUUUUUACCUACCCAGGAA--AAGCCAACCAA-CCUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUAGCUGUCGCUCGGCUGCAUGCCUAGUGCACCUACGCAGUAUAAACAAUAAUAAAUUUUACUGUCGUUGACAAGAAACGAGUAACUCGUCCCUCUUCUGCAGACU
MK062184.1/1-299 AUAUUAGGUUUUUACCUACCCAGGAA--AAGCCAACCAA-CCUCGAUCUCUUGUAGAUCUGUUCUCUAAUGGUCGCUUUAAAA------UCUGUGUAGCUGUCGCUCGGCUGCAUGCCUAGUGCACCUACGCAGUAUAAACAAUAAUAAAUUUUACUGUCGUUGACAAGAAACGAGUAACUCGUCCCUCUUCUGCAGACU
AY559082.1/1-297 AAAUUUUGUUU-CAUCUAUACAGGAA--AAGCCAACCAA-CCUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUAGCUGUCGCUCGGCUGCAUGCCUAGUGCACCUACGCAGUAUAAACAAUAAUAAAUUUUACUGUCGUUGACAAGAAACGAGUAACUCGUCCCUCUUCUGCAGACU
DQ412043.1/1-294 AUAUUAGGUUUUUACCUACCCAGGAA--AAGCCAACCAA-CCUCGAUCUCUUGUAGAUCUGUUCUUUAAACGA-ACUUUAAAA------UCUGUGUGGCUGUCGCUUGGCUGUAUGCCUAGUGCACCUACACAGUAUAAAUAAUA----ACUUUACUGUCGUUGACAAGAAACGGGUAACUCGUCCUUCUUCUGCAGACU
KP886809.1/1-297 AUAUUAGGUUUUUACCUACCCAGGAA--AAGCCAACCAA-CCUCGAUCUCUUGUAGAUCUGUUCUUUAAACGA-ACUUUAAAA------UCUGUGUGGCUGUCGCUCGGCUGUAUGCCUAGUGCACCUACACAGUAUAAAUAUUAAU-AACUUUACUGUCGUUGACAAGAAACGAGUAACUCGUCCUUCUUCUGCAGACU
DQ022305.2/1-295 --GUUAGGUUUUUACCUACCCAGGAA--AAGCCAACCAA-CCUUGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUGGCUGUCGCUCGGCUGCAUGCCUAGCGCACCUACGCAGUAUAAAUAUUAAU-AACUUUACUGUCGUUGACAAGAAACGAGUAACUCGUCCCUCUUCUGCAGACU
MK211374.1/1-294 ---UUAGGUUUUUACCUACCCAGGAA--AAGCCAACCAA-CUUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUGGCUGUCGCUUGGCUGUAUGCCUAGUGCACCUACGCAGUACAAAUAUUAAU-AACUCUAUUGUCGUUGACAAGAAACGAGUAACUCGUCCUUCUUCUGCAGACU
DQ648857.1/1-297 AUAUUAGGUUUUUACCUACCCAGGAA--AAGCCAACCAA-UCUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUAGCUGUCGCUCGGCUGCAUGCCUAGUGCACUUACGCAGUAUAAAUAUUAAU-AACUUUACUGUCGCUGACUGGAUACGAGUAACUCGUCCUUCUUCUGCAGACU
KF569996.1/1-305 AUAUUAGGUUUUUACCUACCCAGGAA--AAGCCAACCAACCCUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAAGCAUUCUCUGUGUAGCUGUCGCUCGGCUGCAUGCCUAGUGCACCUACGCAGUAUAAACAAUAAUAAACUUUACUGUCGUUGACAAGAAACGAGUAACUCGUCCCCCUUCUGCAGACU
MT163718.1/1-299 UUGGUUGGUUUAUACCUUCSCAGGUAACAAACCAACCAACUUUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUGGCUGUCACUCGGCUGCAUGCUUAGUGCACUCACGCAGUAUAAUUAAUAACUAA--UUACUGUCGUUGACAGGACACGAGUAACUCGUCUAUCUUCUGCAGGCU
MT344963.1/1-299 AUUAAAGGUUUAUACCUUCCCAGGUAACAAACCAACCAACUUUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUGGCUGUCACUCGGCUGCAUGCUUAGUGCACUCACGCAGUAUAAUUAAUAACUAA--UUACUGUCGUUGACAGGACACGAGUAACUCGUCUAUCUUCUGCAGGCU
MT019530.1/1-299 AUUAAAGGUUUAUACCUUCCCAGGUAACAAACCAACCAACUUUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUGGCUGUCACUCGGCAGCAUGCCGAGUGCAGCCACACAGUAUAAUUAAUAACUAA--UUACUGUCGUUGACAGGACACGAGUAACUCGUCUAUCUUCUGCAGGCU
MT263421.1/1-296 ---AUAGGUUUAUACCUUCCCAGGUAACAAACCHUUHAACUUUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUGGCUGUCACUCGGCUGCAUGCUUAGUGCACUCACGCAGUAUAAUUAAUAACUAA--UUACUGUCGUUGACAGGACACGAGUAACUCGUCUAUCUUCUGCAGGCU
MT345869.1/1-293 ------GGUUUAUACCUUCCCAGGUAACAAUCCAWUCAACUUUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUGGCUGUCACUCGGCUGCAUGCUUAGUGCACUCACGCAGUAUAAUUAAUAACUAA--UUACUGUCGUUGACAGGACACGAGUAACUCGUCUAUCUUCUGCAGGCU
MT345841.1/1-293 ------CUYYUAUACCUUCCCAGGUAACAAACCHWYCAACUUUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUGGCUGUCACUCGGCUGCAUGCUUAGUGCACUCACGCAGUAUAAUUAAUAACUAA--UUACUGUCGUUGACAGGACACGAGUAACUCGUCUAUCUUCUGCAGGCU
MG772934.1/1-298 AUAUUAGGUUUUUACCUUCCCAGGUAACAAACCAACUAACUCUCGAUCUCUUGUAGAUCUGUUCUCUAAACGA-ACUUUAAAA------UCUGUGUGACUGUCACUUAGCUGCAUGCUUAGUGCACUCACGCAGUUUAAUUA-UAAUUAA--UUACUGUCGUUGACAGGACACGAGUAACUCGUCUAUCUUCUGCAGGUU
#=GC SS_cons     ::::::<<<<<-<<<<<____>>>>>..>>>>>::::::.::::<<<<<_____>>>>>:<<<<_______>>.>>:::::::......:<<<<<<<<-<<-<<<<-<<<_____>>>->>>>>>->>>>>>>>::::::::::::::::::::::::((((((((((((-(((((---(((-(((-((((<<<--<<<<
#=GC RF          AuauuAgGcuuuugCCuaccCaGGca..aagCcAAccAA.uuUcGauCuCUUGUaGauCUGuuCUcUAAAcGa.aCUUUAAAA......UCuGcGuggCuGUCgCucgGCUGcAUGCcuaGcGCacccaCgCaGUAUAAauAaUAAuaAAuUUUAcUGuCGuuGaCagGgaaCgaGUAACuCGuCcauCuuCuGCAGgCu

KU973692.1/1-298 GCUUACGGUUUCGUCCGUGUUGCAGUCGAUCAUCAGCAUACCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUUCUUGGAAUCAACGAGAAAA
DQ071615.1/1-298 GCUUACGGUUUCGUCCGUGUUGCAGUCGAUCAUCAGCAUACCUAGGUUUCGUCCGGGUGUGACCGAGAGGUAAGAUGGAGAGCCUUGUUCUUGGAAUCAACGAGAAAA
KF367457.1/1-298 GCUUACGGUUUCGUCCGUGUUGCAGUCGAUCAUCAGCAUACCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUUCUUGGUGUCAACGAGAAAA
MK211377.1/1-296 GCUUACGGUUUCGUCCGUGUUGCAGUCGAUCAUCAGCAUACCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUUCUUGGUGUCAACGAGAAAA
MK062184.1/1-299 GCUUACGGUUUCGUCCGUGUUGCAGUCGAUCAUCAGCAUACCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUUCUUGGUGUCAACGAGAAAA
AY559082.1/1-297 GCUUACGGUUUCGUCCGUGUUGCAGUCGAUCAUCAGCAUACCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUUCUUGGUGUCAACGAGAAAA
DQ412043.1/1-294 GCUUACGGUUUCGUCCGUGUUGUAGUCGAUCAUCAGCAUACCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUUCUUGGUGUCAACGAGAAAA
KP886809.1/1-297 GCUUACGGUUUCGUCCGUGUUGCAGUCGAUCAUCAGCAUACCUAGGUUCCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUUCUUGGUGUCAACGAGAAAA
DQ022305.2/1-295 GCUUACGGUUUCGUCCGUGUUGCAGUCGAUCAUCAGCAUACCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUUCUUGGUGUCAAUGAGAAAA
MK211374.1/1-294 GCUUACGGUUUCGUCCGUGUCGCAGUCGAUCAUCAGCAUACCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUUCUUGGUGUCAACGAGAAAA
DQ648857.1/1-297 GCUUACGGUUUCGUCCGUGUUGCAGUCGAUCAUCAGCAUACCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGCUCUUGGUGUCAGCGAGAAAA
KF569996.1/1-305 GCUUGCGGUUUCGUCCGUGUUGCAGUCGAUCAUCAGCAUACCUAGGUUCCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUUCUUGGAAUCAACGAGAAAA
MT163718.1/1-299 GCUUACGGUUUCGUCCGUGUUGCAGCCGAUCAUCAGCACAUCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUCCCUGGUUUCAACGAGAAAA
MT344963.1/1-299 GCUUACGGUUUCKUCCGUGUUGCAGCCGAUCAUCAGCACAUCUAGGUUUUGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUCCCUGGUUUCAACGAGAAAA
MT019530.1/1-299 GCUUACGGUUUCGUCCGUGUUGCAGCCGAUCAUCAGCACAUCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUCCCUGGUUUCAACGAGAAAA
MT263421.1/1-296 GCUUACGGUUUCGUCCGUGUUGCAGCCGAUCAUCAGCACAUCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUCCCUGGUUUCAACGAGAAAA
MT345869.1/1-293 GCUUACGGUUUCGUCCGUGUUGCAGCCGAUCAUCAGCACAUCUAGGUUUUGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUCCCUGGUUUCAACGAGAAAA
MT345841.1/1-293 GCUUACGGUUUCGUCCGUGUUGCAGCCGAUCAUCAGCACAUCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUCCCUGGUUUCAACGAGAAAA
MG772934.1/1-298 GCUUACGGUUUCGUCCGUGUUGCAGCCGAUCAUCAGCAUACCUUGGUUUCGUCCGGGUGUGACCGAGAGGUAAGAUGGAGAGCCUUGUCCCUGGUUUCAACGAGAAAA
#=GC SS_cons     <<-<<<<<______>>>>>-->>>>>>------>>><<<<<<<-<<______>>>>>>>>><<<____>>>))))-))))))-))))))))))---))))))):::::
#=GC RF          GCUcaCGGUUUCGUCCGugUUGCaGcCGAUCAUCaGCacacCcAGGUUUcGUCCgGguguGaCCGAAAGGuaaGaUgGaGaGCCucGucCcuGGuuuCaaCGaGAAAA
//
