_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: e-113 Query name: gi|658131689|emb|CCX35038.1| selenoprotein Pa [Oncorhynchus mykiss] Query range: 1-406 (total 406) Target: /data/www-rg/seblastian_results/618074014/tempfiles/temptarget.fasta Chromosome: CM007940.1:subseq_37943124,101414_ Strand: + Positions: -Exon 1 49919 50124 -Exon 2 50290 50502 -Exon 3 50637 50754 -Exon 4 50848 51528 Redox box: YES Query MMWVGLSLLLALCLLPGGGTESEGEGTRCKQPPGWSIGEVEPMKEVMGQVTVVALLQASULFCLVQASL <---Intron---> LDGLRLKLEGQGLEN /|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 165bp > ||||||||||||||| Target VMWVGLSLLLALCLLPGGGTESEGEGTRCKQPPGWSIGEVEPMKEVMGQVTVVALLQASULFCLVQASL LDGLRLKLEGQGLEN gatggcacccgctcccgggagaggggactacccgtaaggggcaaggagcgagggcccgatttttgcgtt tggcccacggcgcga ttgtgtgtttctgttcgggcagagagcggaaccgggtgatactaattgatcttcttacggttgttacct tagtgtatagagtaa ggggaacgcgtccgctgcaagtggagcctggattgttggggtgggcgcgcgggcacgctagccgggac agtggcggggtgtggt * Query VTYMVVNHQGEQAQRLHTLLRQKLSENITLYKQQPKQEDVWQTLAGEKDDFLIYDR <---Intron---> CGRLTYHISLPYSILGTPYVENAIKETY |||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 134bp > |||||||||||||||||||||||||||| Target VTYMVVNHQGEQAQRLHTLLRQKLSENITLYKQQPKQEDVWQTLAGEKDDFLIYDR CGRLTYHISLPYSILGTPYVENAIKETY gataggaccggcgccccaccacactgaaactacccacgggtcacgggaggtcatga tgccatcatccttacgactggagaagat tcatttaaagaacagtacttgaatcaatctaaaacaaaatgactcgaaaatttaag gggtcaatctcacttgccataactaaca gctgggccggggcgcaccggggagtgccgacaagcagatgggcgcaggtcccctc atttgcctccgccccgttctagcccggcc Query CTRVCGDCTYE <---Intron---> SKEIPAECNRTVEAKPEGEEKPVTGRETTHGGHGHHHHGHGHNGNRHGHNGNRHGHDHHGERGMGRGHGRDHG ||||||||||| < 93bp > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Target CTRVCGDCTYE SKEIPAECNRTVEAKPEGEEKPVTGRETTHGGHGHHHHGHGHNGNRHGHNGNRHGHDHHGERGMGRGHGRDHG tacgtggtatg aagacggtaaagggacggggacgagagaacggcgccccgcgcagaccgcagaccgcgccggagagcgcgcgcg gcgtggagcaa gaatccagagctacacagaaactcggaccaggagaaaagagaagagagaagagagaaaagaggtgggaggaag cacctgccgtg cggcaagccgaagagtgagggaccaggatttaccttcttctctcccttctcccttctcttgggggctcttttg Query AERQHQHDTEGLQHGQAHGQLHVGQEHMGQQAVQLGQMPQEGQRGHIMQNPUVKGKSRUKAEHSUQWKEGSDLSPSSKASUCUHURRLFGDGVSNEPIGL ||/||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Target AEQQHQHDTEGLQHGQAHGQLHVGQEHMGQQAVQLGQMPQEGQRGHIMQNPUVKGKSRUKAEHSUQWKEGSDLSPSSKASUCUHURRLFGDGVSNEPIGL ggcccccgaggcccgcgcgctcggcgcagccggccgcaccggccgcaacactgagatataggcatctaggtgcacttagatttctcactggggaagcagc caaaaaaacagtaagacagatatgaaatgaactatgatcaagaggattaacgtagacggacaaggagaagcatgcccacggggagggttgagtgaactgt cgggcatctggcaccgctcggcttggtgtggagagcggcgaggacttggtcaggggcgagggccagggggttatctcgccacacagggtctggccgacgc * * * * * * Query UHCDEALPASUQUQGLIGLRETUQURSSLADUQQPQPVMUAUPLGVESUGUGLL |||||||||||||||||||||||||||||||||||||||||||||||||||||| Target UHCDEALPASUQUQGLIGLRETUQURSSLADUQQPQPVMUAUPLGVESUGUGLL tctgggccgttctcgcagcagatctcttcggtcccccgatgtccgggatgtgcc gagaactcccgagagttgtgacgaggcctcagaacacttgcgctgtagggggtt acttgggcccagagagaccggcagacgcctcaggtgacgacacgttgcagaggg * * * * * * * * * * Sequence until next stop: TAA * Distance CDS-SECIS: 354 ; UGA-SECIS: 363 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = CM007940.1:subseq_37943124,101414_ Strand = + Positions = 51883 - 51952 Found by: Infernal (score=30.9) Covels (score=29.65) Stem2 length = 11 Apical loop length = 14 Insertion in stem2 = 0, 0 Free Energy = -24.04 ..(((((((.......(((((((((((((((...............)))))))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc .((((({((---....{[[(((((((((([(.....-.........)]))))))))))]]}..--.--.))}))))). target CCUCCAUCC---ACAGUGAAGGCAGGCGCAGAAACU-ACGCUCUAGUGGCGUCUGUCUGAUGU--C--CGGCUGGGGA **** ^^^ **** _________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:2 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: e-113 Query name: gi|658131689|emb|CCX35038.1| selenoprotein Pa [Oncorhynchus mykiss] Query range: 1-406 (total 406) Target: /data/www-rg/seblastian_results/618074014/tempfiles/temptarget.fasta Chromosome: CM007940.1:subseq_37943124,101414_ Strand: + Positions: -Exon 1 49919 50124 -Exon 2 50290 50502 -Exon 3 50637 50754 -Exon 4 50848 51528 Redox box: YES Query MMWVGLSLLLALCLLPGGGTESEGEGTRCKQPPGWSIGEVEPMKEVMGQVTVVALLQASULFCLVQASL <---Intron---> LDGLRLKLEGQGLEN /|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 165bp > ||||||||||||||| Target VMWVGLSLLLALCLLPGGGTESEGEGTRCKQPPGWSIGEVEPMKEVMGQVTVVALLQASULFCLVQASL LDGLRLKLEGQGLEN gatggcacccgctcccgggagaggggactacccgtaaggggcaaggagcgagggcccgatttttgcgtt tggcccacggcgcga ttgtgtgtttctgttcgggcagagagcggaaccgggtgatactaattgatcttcttacggttgttacct tagtgtatagagtaa ggggaacgcgtccgctgcaagtggagcctggattgttggggtgggcgcgcgggcacgctagccgggac agtggcggggtgtggt * Query VTYMVVNHQGEQAQRLHTLLRQKLSENITLYKQQPKQEDVWQTLAGEKDDFLIYDR <---Intron---> CGRLTYHISLPYSILGTPYVENAIKETY |||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 134bp > |||||||||||||||||||||||||||| Target VTYMVVNHQGEQAQRLHTLLRQKLSENITLYKQQPKQEDVWQTLAGEKDDFLIYDR CGRLTYHISLPYSILGTPYVENAIKETY gataggaccggcgccccaccacactgaaactacccacgggtcacgggaggtcatga tgccatcatccttacgactggagaagat tcatttaaagaacagtacttgaatcaatctaaaacaaaatgactcgaaaatttaag gggtcaatctcacttgccataactaaca gctgggccggggcgcaccggggagtgccgacaagcagatgggcgcaggtcccctc atttgcctccgccccgttctagcccggcc Query CTRVCGDCTYE <---Intron---> SKEIPAECNRTVEAKPEGEEKPVTGRETTHGGHGHHHHGHGHNGNRHGHNGNRHGHDHHGERGMGRGHGRDHG ||||||||||| < 93bp > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Target CTRVCGDCTYE SKEIPAECNRTVEAKPEGEEKPVTGRETTHGGHGHHHHGHGHNGNRHGHNGNRHGHDHHGERGMGRGHGRDHG tacgtggtatg aagacggtaaagggacggggacgagagaacggcgccccgcgcagaccgcagaccgcgccggagagcgcgcgcg gcgtggagcaa gaatccagagctacacagaaactcggaccaggagaaaagagaagagagaagagagaaaagaggtgggaggaag cacctgccgtg cggcaagccgaagagtgagggaccaggatttaccttcttctctcccttctcccttctcttgggggctcttttg Query AERQHQHDTEGLQHGQAHGQLHVGQEHMGQQAVQLGQMPQEGQRGHIMQNPUVKGKSRUKAEHSUQWKEGSDLSPSSKASUCUHURRLFGDGVSNEPIGL ||/||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Target AEQQHQHDTEGLQHGQAHGQLHVGQEHMGQQAVQLGQMPQEGQRGHIMQNPUVKGKSRUKAEHSUQWKEGSDLSPSSKASUCUHURRLFGDGVSNEPIGL ggcccccgaggcccgcgcgctcggcgcagccggccgcaccggccgcaacactgagatataggcatctaggtgcacttagatttctcactggggaagcagc caaaaaaacagtaagacagatatgaaatgaactatgatcaagaggattaacgtagacggacaaggagaagcatgcccacggggagggttgagtgaactgt cgggcatctggcaccgctcggcttggtgtggagagcggcgaggacttggtcaggggcgagggccagggggttatctcgccacacagggtctggccgacgc * * * * * * Query UHCDEALPASUQUQGLIGLRETUQURSSLADUQQPQPVMUAUPLGVESUGUGLL |||||||||||||||||||||||||||||||||||||||||||||||||||||| Target UHCDEALPASUQUQGLIGLRETUQURSSLADUQQPQPVMUAUPLGVESUGUGLL tctgggccgttctcgcagcagatctcttcggtcccccgatgtccgggatgtgcc gagaactcccgagagttgtgacgaggcctcagaacacttgcgctgtagggggtt acttgggcccagagagaccggcagacgcctcaggtgacgacacgttgcagaggg * * * * * * * * * * Sequence until next stop: TAA * Distance CDS-SECIS: 991 ; UGA-SECIS: 1000 ------- SECIS element -- id:2 -- grade:A ---- Chromosome = CM007940.1:subseq_37943124,101414_ Strand = + Positions = 52520 - 52592 Found by: Infernal (score=25.37) Covels (score=19.02) Stem2 length = 9 Apical loop length = 15 Insertion in stem2 = 0, 1 Free Energy = -23.06 ..(((((((.......(((((((((((((((...............))))))))).))))))........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccagg-cCuGAUGuuuuuucaugaccggc ..((((((((--....{[[(((({((((((......--.........))))))}).)))]]}..--...)))))))).. target CAUUCUGUAC--UUAAUGAAGGGCUCUAGGGGAAGA--CAACUGUCACCUAGAACACCUGAUGC--UUUGUACAGAACA **** ^^ ****