_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:QUE_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 9e-96 Query name: gi|1041103057|ref|XP_017274552.1| PREDICTED: selenoprotein O isoform X1 [Kryptolebias marmoratus] Query range: 1-691 (total 691) Target: /data/www-rg/seblastian_results/507300836/tempfiles/temptarget.fasta Chromosome: SSNR01000209.1:subseq_776635,116323_ Strand: + Positions: -Exon 1 63142 63695 -Exon 2 64012 64215 -Exon 3 64303 64480 -Exon 4 64674 64804 -Exon 5 64897 65174 -Exon 6 65265 65433 -Exon 7 65790 65975 -Exon 8 66155 66311 -Exon 9 66392 66610 Redox box: YES Query MAYLGPRLGTSRLFIPRVSAARLLGTVRMDDMGLAVSRSPLERLDFDNVVLRRLPLDPSEEPGARQVKGACFSRVKPQPLSNPRFVAVSPEALALLGLHA ||| || || ||/|/||/| ||||| || ||| |||||||||/|||/ ||/|||||||||| ||||||||||||||||/ ||||||| ||| |||| Target MAYFGPWLGASRIFLPRLSVFRLLGTFGMDAMGLTVSRSPLERLEFDNMALRKLPLDPSEEPGVRQVKGACFSRVKPQPLNAPRFVAVSREALTLLGLDG agttgctcggtcatcccctgtaccgatgaggagcagactccgccgtgaagcaacccgctggcggacgaggtttcgaccccagcctgggtcggcaccgcgg tcatgcgtgccgtttcgtcttgttgctgtactgtctggcctagtataatctgatctaccaacgtgatagcgtcgtacactaccgttctcgactcttgtag gtccatggagacttcccgcccacctttagccgagggttttgggcatccgctaatcgctcggggggggaagtctaggtgggcctgccgggaacggggacca Query DQVVKDPLGPEYLSGSRVMPGSEPAAHCYCGHQFGHFAGQLGDGAACYLGEVKVPPGQDPELLRENPSGRWEIQVKGAGLTPYSR <---Intron---> |/|| ||||||/||||||||||||||||||||||| ||||||||||||||||||| || |||||||||||||||||||||||||| < 316bp > Target DEVVNDPLGPEFLSGSRVMPGSEPAAHCYCGHQFGQFAGQLGDGAACYLGEVKVPLGQSPELLRENPSGRWEIQVKGAGLTPYSR ggggagccgcgtcagtagacgtgcggctttgcctgctggccgggggttcgggagccgcacgcccgacagctgacgagggcactta aattaactgcattggcgttcgcacccagaggaatgatcgatgagccgatgatatctgagcattgaacggggatatagcgtccacg cacgcctgtggtcctcatgcacacgtcccttcgctgctggtgcgacccgggggtaccaccggcgacgtccggtggagtagcccc Query QADGRKVLRSSIREFLCSEAMFFLGVPTTRAGSVVTSDTKVIRDVYYSGHPKHERCSVVLRLAPTFLR <---Intron---> FGSFEIFKPADELTG ||||||||||||||||||||||||||||||||||| ||//|||||||||||/|||||||||/|||||| < 87bp > |||||||||||| || Target QADGRKVLRSSIREFLCSEAMFFLGVPTTRAGSVVISDSRVIRDVYYSGHPRHERCSVVLRIAPTFLR FGSFEIFKPADEFTG cgggcagcctaaagtctaggattcggcaaaggtggatgaagaaggttagccccgattggccagcatca tgttgatacgggtag acaggattgcgtgattggacttttgtcccgcgctttcaggttgataaggacgaaggctttgtcccttg tgctattaccaatcg aattctgcggctaagcgctgtgccccgcctaattgtctccacaattcccatcttgacatccattcccc atactgccgattacat Query RQGPSYGQDEIRAQMLDYVIEMFYPEIQQNYPNQVERNVAFFRE <---Intron---> VMYRTARLVAQWQCVGFCHGVLNTDNMSVLGLTLDYGPYG |||||||/|||| |||||||| ||||||||||//|/||||||/| < 193bp > ||||||||||||||||||||||||||||/||||||||||| Target RQGPSYGRDEIRGQMLDYVIETFYPEIQQNYPDRVDRNVAFFKE VMYRTARLVAQWQCVGFCHGVLNTDNMSILGLTLDYGPYG ccgcatgcggacgcatgtgagattcgaccatcgcggaaggttag gatcagccggctctggttcggcaagaaaatgcatgtgctg gagcgaggaatggattaattactacataaaacagtagatcttaa ttagccgttcagagtgtgagttacaatgttgtctaagcag tgtcctggtgcatgggttctggcctacggctgcggcatgtccag ggttatacgtgggtaactcatgcaccgccgattacttacc Query FMDR <---Intron---> FDPDFICNASDNSGRYSYQAQPTICRWNLVKLAEALAPELPPDRAEAVMDEYQDLFNRFYLENMRKKLGLLTKEEPEDEI |||| < 92bp > |||||||||||||||||||||||||||||||||||||||||||||||/|||||| |||||||||||||||| |||||||/ Target FMDR FDPDFICNASDNSGRYSYQAQPTICRWNLVKLAEALAPELPPDRAEAIMDEYQDQFNRFYLENMRKKLGLLIKEEPEDEM taga tgcgtatagtgatgctttcgccaatatacgacgggcgcgcccgcgggaaggtcgctacttcgaaaaacgttaaggcggga ttag tacattgaccaacggacaacacctgggattatcactccatccagcacttaaaaaatagtataatgaatgtttaaacaaat cgc gttacctctgcccacacccgcggtccggcggggtgtttaacagtgtacagtacgtgtccccggcggggtcggagggtgtgg Query LITELLQTMHNTG <---Intron---> ADFTNTFRSLSQVSCPTEEEAEGHEE-LKKTTDLVLEQCASLDELKAANKPTMDLR <---Intron---> ||||||||||||| < 90bp > |||||||||/||/||||| / || || /||||||/|/|||||/||||||||||| | < 356bp > Target LITELLQTMHNTG ADFTNTFRSMSQISCPTEGDTEGEEEAVKKTTDLLLDQCASLEELKAANKPTMDPR caagtccaacaag ggtaaatcaaacattcagggagggggggaaaagcccgctgttggcaggaacaagcc ttcattactaac gcatcactggtgatcgccagacagaaactaaccatttaagcctaataccaacctacg gctggggggccg tttcccccacgtgtctgtgactaaagattgacacctttgtccaggcgaccgctgca Query ELSMLLSMAQSNPALFQMISDRVTIARQLDKLSKLKELMETSQEELKTRQAEEWSSWLTRYR <---Intron---> KRLARELEGQSDVQATQEERV ||/|||||||||| |||| ||| ||||||||||| |/|||||||||| /|||||/||/|||| < 179bp > ||||||||||||||| ||||| Target ELAMLLSMAQSNPTLFQMFSDRATIARQLDKLSKTKDLMETSQEELKAKQAEEWTSWITRYR KRLARELEGQSDVQAVQEERV gcgacctagcaacactcattgagaagactgacaaaagcagaacggcagacgggtattaacta accgcgcggcaggcggcggag atctttctcagaccttattcagcctcgataatgacaattacgaaatacaacaagccgtcgag agtcgatagagatactaaagt cgggggccgtgccctgcggcacgggccgggcaccaggcggggtggggacagtgggtcgcatc gacgctgggtgtcggtggaggg Query RVMDSTNPRVVLRNYIAQNAIEAAENSDFSE <---Intron---> VQRVLKVLQKPFSSQPGLELPAWVGGHGTASQAERDEGEEQQHEASASAARNP /|||| |||||||||||||||||||| |||| < 80bp > ||||||||/||||||||||||||| ||||//| |||| |||| | |//||||| Target KVMDSANPRVVLRNYIAQNAIEAAENGDFSE VQRVLKVLEKPFSSQPGLELPAWVSGHGTSAQGERDEAEEQQPEESSAAARNP agagagaccggcaatagcagaggggaggttg gcagcagcgactttccgcgccgtgagcgaagcggcgggggcccggttgggaac attagcacgtttgaatcaactaccaagatca tagttattaactccacgtatccgtggagcgcagagaacaaaacaacccccgac gggcctcttggcgccccgtatgttgttcccg cagccgtggatcctgtcagttgggcacgctaggagcaggaagaagaaaacaca Query VPYNSRPPAWAQEICVTUSS |||/|/|| ||||||||||| Target VPYDSKPPVWAQEICVTUSS gctgaaccgtgcgatgattt tcaagacctgcaatgtcgcc gtcccatacgagactcaata * Sequence until next stop: TAA * Distance CDS-SECIS: 413 ; UGA-SECIS: 419 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = SSNR01000209.1:subseq_776635,116323_ Strand = + Positions = 67024 - 67109 Found by: Infernal (score=24.98) Covels (score=17.07) Stem2 length = 9 Apical loop length = 16 Insertion in stem2 = 0, 0 Free Energy = -14.84 ..(((((((.............(((((((((((((((...............)))))))))))))))............))))))).. model uucggucaugcg------UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu---u-uuucaugaccggc .((((({((.............{[[{(({(((((((......-..........)))))))}))}]]}........-...))}))))). target UUGGUGUCAUUUUUGCUAUUUAUGAUGAUUCAGGCAACAAGU-CGUAAUGAGCUGCCUGAUUCUGACGAGCUAUG-GGCUGUCACUGU **** ^^ **** _________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:2 SeB_exonerate category:QUE_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 9e-96 Query name: gi|1041103057|ref|XP_017274552.1| PREDICTED: selenoprotein O isoform X1 [Kryptolebias marmoratus] Query range: 1-691 (total 691) Target: /data/www-rg/seblastian_results/507300836/tempfiles/temptarget.fasta Chromosome: SSNR01000209.1:subseq_776635,116323_ Strand: + Positions: -Exon 1 50000 50553 -Exon 2 50870 51073 -Exon 3 51161 51338 -Exon 4 51532 51662 -Exon 5 51755 52032 -Exon 6 52123 52291 -Exon 7 52648 52833 -Exon 8 53013 53169 -Exon 9 53250 53468 Redox box: YES Query MAYLGPRLGTSRLFIPRVSAARLLGTVRMDDMGLAVSRSPLERLDFDNVVLRRLPLDPSEEPGARQVKGACFSRVKPQPLSNPRFVAVSPEALALLGLHA ||| || || ||/|/||/| ||||| || ||| |||||||||/|||/ ||/|||||||||| ||||||||||||||||/ ||||||| ||| |||| Target MAYFGPWLGASRIFLPRLSVFRLLGTFGMDAMGLTVSRSPLERLEFDNMALRKLPLDPSEEPGVRQVKGACFSRVKPQPLNAPRFVAVSREALTLLGLDG agttgctcggtcatcccctgtaccgatgaggagcagactccgccgtgaagcaacccgctggcggacgaggtttcgaccccagcctgggtcggcaccgcgg tcatgcgtgccgtttcgtcttgttgctgtactgtctggcctagtataatctgatctaccaacgtgatagcgtcgtacactaccgttctcgactcttgtag gtccatggagacttcccgcccacctttagccgagggttttgggcatccgctaatcgctcggggggggaagtctaggtgggcctgccgggaacggggacca Query DQVVKDPLGPEYLSGSRVMPGSEPAAHCYCGHQFGHFAGQLGDGAACYLGEVKVPPGQDPELLRENPSGRWEIQVKGAGLTPYSR <---Intron---> |/|| ||||||/||||||||||||||||||||||| ||||||||||||||||||| || |||||||||||||||||||||||||| < 316bp > Target DEVVNDPLGPEFLSGSRVMPGSEPAAHCYCGHQFGQFAGQLGDGAACYLGEVKVPLGQSPELLRENPSGRWEIQVKGAGLTPYSR ggggagccgcgtcagtagacgtgcggctttgcctgctggccgggggttcgggagccgcacgcccgacagctgacgagggcactta aattaactgcattggcgttcgcacccagaggaatgatcgatgagccgatgatatctgagcattgaacggggatatagcgtccacg cacgcctgtggtcctcatgcacacgtcccttcgctgctggtgcgacccgggggtaccaccggcgacgtccggtggagtagcccc Query QADGRKVLRSSIREFLCSEAMFFLGVPTTRAGSVVTSDTKVIRDVYYSGHPKHERCSVVLRLAPTFLR <---Intron---> FGSFEIFKPADELTG ||||||||||||||||||||||||||||||||||| ||//|||||||||||/|||||||||/|||||| < 87bp > |||||||||||| || Target QADGRKVLRSSIREFLCSEAMFFLGVPTTRAGSVVISDSRVIRDVYYSGHPRHERCSVVLRIAPTFLR FGSFEIFKPADEFTG cgggcagcctaaagtctaggattcggcaaaggtggatgaagaaggttagccccgattggccagcatca tgttgatacgggtag acaggattgcgtgattggacttttgtcccgcgctttcaggttgataaggacgaaggctttgtcccttg tgctattaccaatcg aattctgcggctaagcgctgtgccccgcctaattgtctccacaattcccatcttgacatccattcccc atactgccgattacat Query RQGPSYGQDEIRAQMLDYVIEMFYPEIQQNYPNQVERNVAFFRE <---Intron---> VMYRTARLVAQWQCVGFCHGVLNTDNMSVLGLTLDYGPYG |||||||/|||| |||||||| ||||||||||//|/||||||/| < 193bp > ||||||||||||||||||||||||||||/||||||||||| Target RQGPSYGRDEIRGQMLDYVIETFYPEIQQNYPDRVDRNVAFFKE VMYRTARLVAQWQCVGFCHGVLNTDNMSILGLTLDYGPYG ccgcatgcggacgcatgtgagattcgaccatcgcggaaggttag gatcagccggctctggttcggcaagaaaatgcatgtgctg gagcgaggaatggattaattactacataaaacagtagatcttaa ttagccgttcagagtgtgagttacaatgttgtctaagcag tgtcctggtgcatgggttctggcctacggctgcggcatgtccag ggttatacgtgggtaactcatgcaccgccgattacttacc Query FMDR <---Intron---> FDPDFICNASDNSGRYSYQAQPTICRWNLVKLAEALAPELPPDRAEAVMDEYQDLFNRFYLENMRKKLGLLTKEEPEDEI |||| < 92bp > |||||||||||||||||||||||||||||||||||||||||||||||/|||||| |||||||||||||||| |||||||/ Target FMDR FDPDFICNASDNSGRYSYQAQPTICRWNLVKLAEALAPELPPDRAEAIMDEYQDQFNRFYLENMRKKLGLLIKEEPEDEM taga tgcgtatagtgatgctttcgccaatatacgacgggcgcgcccgcgggaaggtcgctacttcgaaaaacgttaaggcggga ttag tacattgaccaacggacaacacctgggattatcactccatccagcacttaaaaaatagtataatgaatgtttaaacaaat cgc gttacctctgcccacacccgcggtccggcggggtgtttaacagtgtacagtacgtgtccccggcggggtcggagggtgtgg Query LITELLQTMHNTG <---Intron---> ADFTNTFRSLSQVSCPTEEEAEGHEE-LKKTTDLVLEQCASLDELKAANKPTMDLR <---Intron---> ||||||||||||| < 90bp > |||||||||/||/||||| / || || /||||||/|/|||||/||||||||||| | < 356bp > Target LITELLQTMHNTG ADFTNTFRSMSQISCPTEGDTEGEEEAVKKTTDLLLDQCASLEELKAANKPTMDPR caagtccaacaag ggtaaatcaaacattcagggagggggggaaaagcccgctgttggcaggaacaagcc ttcattactaac gcatcactggtgatcgccagacagaaactaaccatttaagcctaataccaacctacg gctggggggccg tttcccccacgtgtctgtgactaaagattgacacctttgtccaggcgaccgctgca Query ELSMLLSMAQSNPALFQMISDRVTIARQLDKLSKLKELMETSQEELKTRQAEEWSSWLTRYR <---Intron---> KRLARELEGQSDVQATQEERV ||/|||||||||| |||| ||| ||||||||||| |/|||||||||| /|||||/||/|||| < 179bp > ||||||||||||||| ||||| Target ELAMLLSMAQSNPTLFQMFSDRATIARQLDKLSKTKDLMETSQEELKAKQAEEWTSWITRYR KRLARELEGQSDVQAVQEERV gcgacctagcaacactcattgagaagactgacaaaagcagaacggcagacgggtattaacta accgcgcggcaggcggcggag atctttctcagaccttattcagcctcgataatgacaattacgaaatacaacaagccgtcgag agtcgatagagatactaaagt cgggggccgtgccctgcggcacgggccgggcaccaggcggggtggggacagtgggtcgcatc gacgctgggtgtcggtggaggg Query RVMDSTNPRVVLRNYIAQNAIEAAENSDFSE <---Intron---> VQRVLKVLQKPFSSQPGLELPAWVGGHGTASQAERDEGEEQQHEASASAARNP /|||| |||||||||||||||||||| |||| < 80bp > ||||||||/||||||||||||||| ||||//| |||| |||| | |//||||| Target KVMDSANPRVVLRNYIAQNAIEAAENGDFSE VQRVLKVLEKPFSSQPGLELPAWVSGHGTSAQGERDEAEEQQPEESSAAARNP agagagaccggcaatagcagaggggaggttg gcagcagcgactttccgcgccgtgagcgaagcggcgggggcccggttgggaac attagcacgtttgaatcaactaccaagatca tagttattaactccacgtatccgtggagcgcagagaacaaaacaacccccgac gggcctcttggcgccccgtatgttgttcccg cagccgtggatcctgtcagttgggcacgctaggagcaggaagaagaaaacaca Query VPYNSRPPAWAQEICVTUSS |||/|/|| ||||||||||| Target VPYDSKPPVWAQEICVTUSS gctgaaccgtgcgatgattt tcaagacctgcaatgtcgcc gtcccatacgagactcaata * Sequence until next stop: TAA * Distance CDS-SECIS: 413 ; UGA-SECIS: 419 ------- SECIS element -- id:2 -- grade:A ---- Chromosome = SSNR01000209.1:subseq_776635,116323_ Strand = + Positions = 53882 - 53967 Found by: Infernal (score=24.98) Covels (score=17.07) Stem2 length = 9 Apical loop length = 16 Insertion in stem2 = 0, 0 Free Energy = -14.84 ..(((((((.............(((((((((((((((...............)))))))))))))))............))))))).. model uucggucaugcg------UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu---u-uuucaugaccggc .((((({((.............{[[{(({(((((((......-..........)))))))}))}]]}........-...))}))))). target UUGGUGUCAUUUUUGCUAUUUAUGAUGAUUCAGGCAACAAGU-CGUAAUGAGCUGCCUGAUUCUGACGAGCUAUG-GGCUGUCACUGU **** ^^ ****