# STOCKHOLM 1.0
#=GF ID gCoV-5UTR
#=GF AC RF03118
#=GF DE Gammacoronavirus 5'UTR
#=GF AU Lamkiewicz K; 0000-0002-6375-6441
#=GF GA 124.9
#=GF NC 117.4
#=GF TC 157.8
#=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 30.00 -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 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 [2]
#=GF RM 25307890
#=GF RT RNA structure analysis of alphacoronavirus terminal genome regions.
#=GF RA Madhugiri R, Fricke M, Marz M, Ziebuhr J
#=GF RL Virus Res. 2014;194:76-89.
#=GF CC The 5' UTR of gammacoronaviruses is similar to the 5' UTRs of alpha- and
#=GF CC betacoronaviruses, as they also contain 3 helices denoted as SL1, SL2 and
#=GF CC SL4. Further, in a subset of gammacoronaviruses a third stem-loop, SL3, is
#=GF CC observed. SL1 and SL2 have major impacts of the level of viral
#=GF CC replication, whereas SL4 is hypothesized to play a role as a "spacer"
#=GF CC during the template-switch of CoV sgRNA synthesis.
#=GF WK Coronavirus_5'_UTR
#=GF SQ 3

NC_001451.1/1-200 --ACUUAAGAUAGAUAU------UAAUAUAUAUCUAUUA-CACUAGCCUUGCGCUAGA---UUUUUAACUUAACAA-AACGGAC---------UUAAAU--ACCUACAGCUGGUCCUCAUAGGUGUUCCAUUGCAGUGCACUUUAGUGCC----CUGGAUGGCACCUGGCCACCUGUCAGGUUUUUGUUAUUAAAAUCUU
NC_010800.1/1-200 --ACUUAAGAUAGAUAU------UAAUAUAUAUCUAUCA-UACUAGCCUUGUGCUAGA---UUUCCAACUUAACAA-AACGGAC---------UUAAAU--ACCUACAGCUGGUCCUCAUAGGUGUUCCAUUGCAGUGCACUUUAGUGCC----CUGGAUGGCACCUGGCCACCUGUCAGGUUUUUGUUAGUAAAAUAAC
NC_010646.1/1-200 CUAUUUGUGAAUAAUAUAUAUAUAUAUAUAUAUCAUUCAUUCGUUUACCCUUGUGGCAAACAACCCAAAUUAAACAAAACGGACUUGGGUGUGUUUCCUGACCGCACGCGAGUGG-----GGGGUGGCAGCUGAGAGGCACUUUUGUGUCGGCUUCUGGGCCACCUCUUGUGGGUGU-GUGGGGACC---------UGUC
#=GC SS_cons      ..::::::<<<<<<<<<......______>>>>>>>>>:.(((((((,,,,,,,,,,,...,,,<<__________.___>>,,.........,,<<<-..<<<<<<<<-<<<<<-----<<<<<<<--<<<-<<<-<<<<____>>>>-....>>>>>>>>>>>>>>>>>>->>>>->>>>>>>,,,,,,,,,,,,,,,
#=GC RF           ..AcUUaaGAuaGAUAU......uaAUAUAUAUCuaUCA.uccuagcCuuguGcuagA...uuuccAAcUUAAcaA.AACggAC.........UUaccU..cCccACagcuGgccCUCAUgGGggggCcacuGcgguGCACUUUaGUGCC....ccggguccccCCcggcCaccuGUCggGggguugUUAuUAAAAUauc

NC_001451.1/1-200 AUUGUUGCUGGUAUCACUGCUUGUUUUG
NC_010800.1/1-200 AUUGUUGCUGGUAUCACUGCUUGUUUUG
NC_010646.1/1-200 AGAGUUCAGGCGACC-------------
#=GC SS_cons      ,,,,,,))))))):::::::::::::::
#=GC RF           AuuGUUgcugggauCACUGCUUGUUUUG
//
