# STOCKHOLM 1.0
#=GF ID SECIS_1
#=GF AC RF00031
#=GF DE Selenocysteine insertion sequence 1
#=GF AU Griffiths-Jones SR; 0000-0001-6043-807X
#=GF GA 35.0
#=GF NC 34.9
#=GF TC 35.0
#=GF PI SECIS
#=GF SE Gautheret D, PMID:12458087
#=GF SS Published; PMID:12458087
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 28.55 -Z 2958934 CM SEQDB
#=GF DR SO; 1001274; SECIS_element;
#=GF DR GO; 0001514; selenocysteine incorporation;
#=GF RN [1]
#=GF RM 8634917
#=GF RT A novel RNA structural motif in the selenocysteine insertion element of
#=GF RT eukaryotic selenoprotein mRNAs.
#=GF RA Walczak R, Westhof E, Carbon P, Krol A
#=GF RL RNA 1996;2:367-379.
#=GF RN [2]
#=GF RM 12458087
#=GF RT A survey of metazoan selenocysteine insertion sequences.
#=GF RA Lambert A, Lescure A, Gautheret D
#=GF RL Biochimie 2002;84:953-959.
#=GF CC The incorporation of selenocysteine into a protein sequence is directed by
#=GF CC an in-frame UGA codon (usually a stop codon) within the coding region of
#=GF CC the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in
#=GF CC the 3' UTR that is required for the distinction of UGA stop from UGA
#=GF CC selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60
#=GF CC nt in length and adopts a hairpin structure which is sufficiently
#=GF CC well-defined and conserved to act as a computational screen for
#=GF CC selenoprotein genes [2].
#=GF WK SECIS_element
#=GF SQ 61

X13710.1/946-1008         U-UUUCAUC--UAUGAGGGUGUUUCCUCUAAA--CCUACG---AGG-----------GAGGAA-C-A-CCUGAU---CUUA-----CAGAAAA
X12367.1/703-764          G-UUUUUCC---AUGACGGUGUUUCCUCUAAA--UUUAC----AUG-----------GAGAAA-C-A-CCUGAU-UUCCAG------AAAAAU
X03920.1/1172-1235        G-GUUCUUC--CAUGAUGGUGUUUCCUCUAAA--UUUGC----ACG-----------GAGAAA-C-A-CCUGAU-UUCCAG-----GAAAAUC
X13684.1/700-760          U-UUUGCCC---AUGAAGGUGUUCCCUCUAAA--CCUAC----GUG-----------GAGGAA-U-G-CCUGAU-GUCCAG-------GAAAA
AF532927.1/678-740        A-UUUUAUC--CAUGAAAGUGUUUCCUCUAAA--CCUAU----GUG-----------GAGGAA-C-A-CCUGAU-GUCCAG------GAAAAU
L37762.1/2940-3006        C-UCGCUAU---AUGACGAUGGCAAUC-UCAA--AUGUU----CAU--U--------GGUUGC-C-A-UUUGAU--GAAAUCAGUUUUGUGUG
X53463.1/847-903          U-UCACAGA---AUGAUGGCACCUUCC-UAA---ACCCU----CAU-----------GGGUGG-U-G-UCUGAG--AGGC--------GUGAA
X58295.1/1384-1453        U-GGCGUCUU-CAUGAGGGAGGGGCCC--AAA-GCCCUUG--UGGG--C--------GGACCU-C-C-CCUGAG---CCUGUCUGAGGGGCCA
X84742.1/5239-5302        G-UGUCUCU---AUGAAGGAGGGGCCC-GAAG-CCCUUGU---GGG--C--------GGGCCU-C-C-CCUGAG---CCCG----UCUGUGGU
X71973.1/730-791          C-CGGCACU--CAUGACGGCCUGCCUG-CAAA--CCUGC----UGG--U--------GGGGCA-G-A-CCCGAA-AAUCCA-------GCGUG
AB030643.1/4176-4241      C-CGGCACU--CAUGAAGGUCUGCCUG-AAAA-CCAGCCU--GCUG-GU--------GGGGCA-G-U-CCUGAG-GACCUG-------GCGUG
AF274027.1/835-900        C-CGGCACU--CAUGAAGGUCUGCUUG-AAAA-CCAGCCU--GCUG-GU--------GGGGCA-G-U-CCUGAG-GACCUG-------GCGUG
L24896.1/600-665          C-CGGCACU--CAUGACGGUCUGCCUG-AAAA-CCAGCCC--GCUG-GU--------GGGGCA-G-U-CCCGAG-GACCUG-------GCGUG
AB017534.1/661-726        C-CCGGUGCC-UAUGACGGUCUGUCUG-AAAA-CCAGCCC---CUG-GU--------GGGGCA-G-A-CCUGAG-AACCUG-------GCGUG
X76008.1/2709-2772        C-UGGCACC--CAUGACAGUCUGCCUA-AAAA-CCAGCC----CUG-GU--------GGGGCA-G-A-CUCGAG-AACCUG-------GCGUG
L12743.1/694-758          C-UGGCACC--CAUGACAGUCUGCCUA-AAAA-CCAGCCC---CUG-GU--------GGGGCA-G-A-CUCGAG-AACCUG-------GCGUG
AF333036.1/2190-2249      C-AUGCGUC--CAUGAAGUCACUGGCC-UCAA-GCCCAA----GUG-GU--------GGGCAG-U-G-ACAGAA---GA---------GCUGC
AF166127.1/1919-1981      G-CCGGAUG---AUGACGACCUGGGUG-GAAA-CCUACCC-UGUGG--G--------CACCCA-U-G-UCCGAG---CCCC-------CUGGC
AF072865.1/1887-1947      G-UCAGAUG---AUGACGGCCUGUGCA-GAAA-CCCCCAC-GUGGG--C--------UGC-CA-G-G-UUUGAA---CCC--------CUGGC
AF136399.1/1808-1868      G-UCAGAUG---AUGAUGGCCUGGGCA-GAAA-CCCCAUG--UGGG--C--------CGCCCA-G-G-UUUGAA---CCC--------CUGGC
AB022283.1/1669-1729      G-CCAGAUG---AUGAGGACCUGUGCG-GAAA-CCCCCCG--CGGG--C--------UGCCCA-U-G-UCUGAG---CCC--------CUGGC
AF053984.1/1951-2017      G-AUGCGUC--CAUGAAGUCACCAGCC-CCAA-GCCCCUC---GUG-GU--------GGGUGG-U-G-AUGGAA-CCGUCA-----AAGCAGU
S48220.1/1731-1788        U-AUUUGUU--UAUGAUGGCCACAGCC-UAAA--GUACA----CAC-----------GGCUGU-G-A-CUUGAU---UCA--------AAAGA
AL645723.11/192421-192359 U-AUUUGUG--UAUGAUGGUCACAGUG-UAAA--GUUCC----CAC-----------AGCUGU-G-A-CUUGAU--UUUUA----AAAAUGUC
X57999.1/1526-1586        A-UAUUUGUU-UAUGAUGGUCACAGUG-UAAA--GUUCA----CAC-----------AGCUGU-G-A-CUUGAU--UUUUA-------AAAAU
Y11110.1/1218-1277        U-AUUUGUC---AUGACAGUCACAGCA-UAAA--GCGCA----GAC-----------GGCUGU-G-A-CCUGAU--UUUAG------AAAAUA
Y11109.1/927-987          U-GUUUAUU--AAUGACGGCUACAGAU-UAAA--CCUUU----AGC-----------CUCUGG-A-G-CCAGAU--GCAUU------CAAACA
Y11109.1/1272-1330        G-UUUCUCA---GUGAAGGCUACAGAU-UAAA--CCUCU----GGC-----------CUCUGG-A-G-CCAGAU--GCAUU-------GAAAC
AL049837.4/130674-130738  G-UGUGCGG---AUGAUAACUACUGAC-GAAA-GAGUCAU-CGACU--C-------AGUUAGU-G-G-UUGGAU---GUAG------UCACAU
AF093774.1/5851-5916      G-UGUGCGG---AUGAUAACUACUGAC-GAAAGAGUCAUC---GAC--C-----UCAGUUAGU-G-G-UUGGAU---GUAG------UCACAU
AF096875.1/5504-5568      G-UGUGCGA---AUGAUAACUACUGAC-GAAA-GAGCUGU-CUGCU--C-------AGUCUGU-G-G-UUGGAU---GUAG------UCACAC
AF125575.1/5781-5843      G-UGUGUUU---AUGAAGAGCACUAAC-AAAA-GAGUAAU-UGACU--C-------AGUUGGU-G-U-UCAGAU--GCU---------CUCAC
S79854.1/1605-1666        C-ACUGCUG---AUGACGAACUAUCUC-UAAC-UGGUCUU--GACC--A-------CGAGCUA-G-U-UCUGAA---UU-G-------CAGGG
Y11273.1/1139-1211        U-AUUUCUU--UGUGAUGACCGAUUUU-GAAA-UGGGUUU---CUC--UAAUGCCAGGAAAUC-GUG-UCUGAU---GUUG-----UCAAGUA
L28111.1/1299-1365        G-UGUUUGCA-AAUGACGACCGAUUUU-GAAA-UGGUCUCACGGCC--A-------AAAACUC-GUG-UCCGAC---AUC--------AACCC
Y11111.1/1260-1324        G-UGUCUCU---GUGAAGUUCGGUUUU-UAAA-AGGGUCA---UCC--A-------GAAAACC-G-ACACUGAU--GUUUC------CGACAC
M63574.1/1465-1528        G-UUACAUU--GAUGAGAACAGAAACA-UAAA--CUAUGA-CCUAG-G---------GGUUUC-U-G-UUGGAU--AGCUC-------GUAAU
AF322071.1/1577-1642      A-UGUGGUCUUUAUGAAGGCAGGUGCA-GAAA-CUAUGCA---CUA-GU--------GGUGUC-U-G-UCUGAU--GUUUG-------GCCAU
D25220.1/1493-1556        C-UUGCGUU--AAUGAGAACAGAAACG-AAAA--CUAUAA-CCUAG-G---------GGUUUC-U-G-UUGGAU--GGUUG-------GCAAC
D88033.3/5711-5774        C-UUGCGUU--AAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G---------GGUUUC-U-G-UUGGAU--GGUUG-------GCAAC
AF021345.1/10097-10160    G-UUACAUU--AAUGAGAACAGAAACA-UAAA--CUAUGA-CCUAG-G---------GGUUUC-U-G-UUGGAU--AGCUU-------GUAAU
AL833145.1/1479-1545      U-UUGCUUU--AAUGAGAAUAGAAACG-UAAA--CUAUGA-CCUAG-G---------GGUUUC-U-G-UUGGAU-AAUUAG-----CAGUUUA
AB032826.1/1401-1464      ACUUGCGUU--AAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G---------GGUUUC-U-G-UUGGAU--GGUUG-------GCAA-
U43286.1/2054-2120        C-UCUGUUA---AUGACGUCUCUCCCUCUAAA-CCCCAUU-AAGGA--C--------UGGGAG-A-G-GCAGAGCAAGCCU-------CAGAG
U43285.1/2009-2075        C-UCUGAUA---AUGAUGUCUCUCCCU-CUAA-CUCCCAGUAAGGA--C--------UGGGAG-A-G-GCUGAACAAACCU-------CAGAG
AC092237.1/57223-57161    C-AUUCAACU-UAUGAGGAUUAUUUCU-UAAA-GGCCUCU---GGC--U-------CGGAAAU-A-G-UCUGAA---CCU--------UAUUG
U67171.1/375-442          G-ACGCUUC---AUGAUAGGAAGGACU-GAAA-AGUCUUG-UGGAC--A-----CCUGGUCUU-U-C-CCUGAU--GUUCU------CGUGGC
U25264.1/366-432          G-CCGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUCA-AAGAC--C-----UGUGGUCUU-U-C-UUCGAU--GUUCU-------GCGGC
AF241527.2/359-424        G-CCGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUUA---GAC--C-----UGUGGUCUU-U-C-CUCGAU--GUUCC------UGCGGC
AC002327.1/156204-156268  C-UCAGCAG--GAUGAUGAGAAGGGCU-GAAA-UGCUGCC--AAAC--C-------AGGUCCU-U-U-UCUGAU--GGUGG-------CUGGG
AF380118.1/366-433        G-ACGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUUG-UGGAC-GC------CUGGUCCU-U-C-CCUGAU--GUUCU------CAUGGC
U67853.1/375-442          G-ACGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUCU-UGGAC-GC------CUGGUCCU-U-C-CUUGAU--GUUCU------CACGGC
AF390544.1/1076-1142      U-UUGCAUU--AAUGAGGAUUACACAG-AAAA-CCUUUGU--UAAGGGU--------UUGUGUCG-A-UCUGCU--AAUUG-------GCAAA
AF288740.1/1291-1357      U-UUGCAUU--AAUGAGGAUUACACAG-AAAA-CCUUUGU--UAAG-GA-------CUUGUGU-AGA-UCUGAU--AAUUG-------GCAAA
BC003127.1/865-928        G-UCACUGC---AUGAUCCGCUCUGGU-CAAA-CCCUUCC---AGG--C------CAGCCAGA-G-U-GGGGAU--GGUCU-------GUGAC
AF195142.1/461-524        G-UCACCGA---AUGAUCUGCUCUGGU-CAAA-UCCUUCU---AUG--C------CAGCCAGG-G-U-GGUGAU--GACCC-------GUGAC
AF195141.1/689-759        G-ACUGACAU-UAUGAAGGCCUGUACU-GAAG-ACAGCAA--GCUG--U-------UAGUACA-G-A-CCAGAU--GCUUU--CUUGGCAGGC
AY119185.1/838-902        G-AGCC-CU---AUGAUCGAUGAUUGG-CAAA-UCCUCUC--GAGG--A-------ACCGAUC-G-U-UGAGAA--CCCCU-----UUGCCUU
AY060611.1/560-627        G-UGGCGCU--UAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GC--------GGGCAA-U-U-GCUGAU---UACG---AUUAACCAC
AF201385.1/3055-3117      G-CCAGAUG---AUGACGACCUGGGUG-GAAA-CCUACCC-UGUGG--G--------CACCCA-U-G-UCCGAG---CCCC-------CUGGC
AF148217.1/2209-2272      G-AGGCAGCUUUGUGACGACCUUUGGC-UAAA-CUCCAUC--GUGA-GC--------GCCUCU-G-G-UCUGAU---GC---------GCCUC
#=GC SS_cons              <.<<<<---..------<<<<<<<<<<.----.-<<<___.._>>>..-........>>>>>>.>.>.>>----..-----.......>>>>>
#=GC RF                   g.ucucauu..uAUGAcGgccugaccc.uAAA.ccccucu..gggg..c........ggguca.g.g.cCUGAU..gcuug.......gagac
//
