_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 2e-50 Query name: gi|658131683|emb|CCX35035.1| thioredoxin reductase 3a [Oncorhynchus mykiss] Query range: 1-603 (total 603) Target: /data/www-rg/seblastian_results/667643668/tempfiles/temptarget.fasta Chromosome: JACSYO010000324.1:subseq_0,100000_ Strand: + Positions: -Exon 1 14528 14644 -Exon 2 15355 15415 -Exon 3 16227 16336 -Exon 4 16591 16698 -Exon 5 16808 16880 -Exon 6 17024 17143 -Exon 7 17288 17430 -Exon 8 18416 18531 -Exon 9 18701 18926 -Exon 10 19267 19359 -Exon 11 20442 20518 -Exon 12 21973 22129 -Exon 13 22967 23074 -Exon 14 23189 23284 -Exon 15 23367 23501 -Exon 16 25356 25421 Redox box: no Query MPPIDNDTGRNQLKTRIQELIDSNQVLVFSKSHCPFCVK <---Intron---> VKDLFKELNVNCNVVELDLID <---Intron---> EGSNYQEL ||||/||||/|/|| |||/||||| |/|||||/||/||| < 710bp > || ||||||| |||||||||/ < 811bp > /|/||||/ Target MPPIENDTGKNELKCRIQQLIDSNPVMVFSKSYCPYCVK VKALFKELNVECNVVELDLIE DGTNYQEM accagagagaagcatcacccagtacgagtaaattcttga gagttagcaggtagggtgcag ggaatcga tcctaaacgaaataggtaattacacttttgagagcagta tacttaatatagattatatt aagcaaaat gtccatccggtacatgaggtccccaggcctgcctgctcg gacgcaggcggtcggggtcc gtacccggg Query LLEMTRQKTVPNVFVNKTHIGGCDKTMQ <---Intron---> AHKDGILQKLLCGENEVYEYDLIVIGGGSGGLACSK <---Intron---> EAAT ||||| ||/|||||/||||/|||||||| < 254bp > ||/|| |//||||/ | ||||||||||||||||||| < 109bp > |||| Target LLEMTGQKSVPNVFINKTHVGGCDKTMQ AHEDGSLKQLLCGDAEAYEYDLIVIGGGSGGLACSK EAAT ccgaagcaagcagtaaaacgggtgaaac gcgggacaccctgggggtgtgcagagggtggcgtta ggga ttatcgaagtcatttaacatgggaacta caaaggtaattggacacaaaattttgggcggtcgca accc gcggcaaattccccccggcctctcaggg tcacccgggcgccccatcgccgcccaagcacgccag attg Query LGKKVMVLDYVVPTPKGNSWG <---Intron---> LGGTCVNVGCIPKKLMHQTALLGTSIQDARKFGWEVPEETV <---Intron---> KHNWET ||||||||||||||||| /|| < 143bp > ||||||||||||||||||||/||||/||||||||| ||| < 144bp > ||||/| Target LGKKVMVLDYVVPTPKGTTWG LGGTCVNVGCIPKKLMHQTAVLGTSMQDARKFGWEF-SETV KHNWDT tgaagagcgtggcacagaatg cggatgaggtacaacaccaggcgatacggcatgtgt-agag acatga tgaattttaattcccagccg gtggcgtatggtcaattaaccttgcctaacgatggat-gac taaagac ggggcgagcttgcatgaccg tccactgcgcctcggggcgacggcccggcgcgccggc-cga ggccgcg Query MKTAVNNYIGSLNWGYRVALRDKNVNYVNSYAEFIEPHKIK <---Intron---> ATNKRGKETFHTAAKFILATGERPRYLGIPGDKEYCITS <-- |||||||||||||||||||||||||||||/|||||||||/| < 985bp > ||||||||||||||||||||||||||||||||||||||| < Target MKTAVNNYIGSLNWGYRVALRDKNVNYVNAYAEFIEPHKVK ATNKRGKETFHTAAKFILATGERPRYLGIPGDKEYCITS aaaggaatagtcatgtaggcagaagatgagtggtagccaga gaaacgagatcaggatatgaggacctcgacggagttaaa tacctaaatgctaggagtctgaaataatacacattacaata ccaaggaactacccatttccgagcgatgtcgaaaagtcg gggggcccccagcgccggaggcgtcctccctagctaacacg gccagggggtcggggtcgtttgggccgcctacggcccc Query -Intron---> DDLFSLPHCPGKTLVIGASYVALECGGFLAGLGLDVTVMVRSILLRGFDQDMANRAGEHMEEHGVKFLRKYVPVK <---Intron-- 169bp > |||||| |||||||||||||||||||||||||||||||||||||||||||/|||||||||||||||||||||||| < 340bp Target DDLFSLSHCPGKTLVIGASYVALECGGFLAGLGLDVTVMVRSILLRGFDQEMANRAGEHMEEHGVKFLRKYVPVK ggcttttctcgaacgaggttggcgtggtcggcgcggagagctaccagtgcgagacgggcaggcggatccatgcga aattctcagcgactttgccatctagggttcgtgtatctttgctttggtaaatcagcgaataaagtattgaatcta cccccggcccgagcggcaggcggggcctcgccgtcccccgccccgggcccaagcctcggcgggcccacgcacccgg Query -> VEELEAGTPGRLKVTAKSTESDETIEGEYNT <---Intron---> VLIAVGRDACTGKIGLDQAGVKVNPK <---Intron---> NGKVPVND > |||||||||||||||||||||/| ||||||| < 1082bp > ||||||||||| |/|||/ ||||||| < 1454bp > |||||||| Target VEELEAGTPGRLKVTAKSTESEEIIEGEYNT VLIAVGRDACTDKVGLDKIGVKVNPK NGKVPVND gggcgggacgacagagatagaggaagggtaa gcagggcggtagaggcgaaggagaca agagcgag taatacgccggtatccaccagaattagaaac tttctggacgcaatgtaatgtataca agatctaa agggaactccgggggcgcagcggccgagccg ggaagcacacccgccgcgagcaccc atggtggct Query EEQTNVPHIYAIGDILEGKWELTPVAIQAGKLLARRLYAGASLK <---Intron---> CDYVNVPTTVFTPLEYGACGHSEEKAIELYGQDNLE <-- |||||||||||||||||||||||||||||||||||||| |//|| < 837bp > |||||||||||||||||/|| |||/| ||||||||| < Target EEQTNVPHIYAIGDILEGKWELTPVAIQAGKLLARRLYKGSTLK CDYVNVPTTVFTPLEYGSCGLSEERATELYGQDNLE ggcaagccatgaggacggatgcacggacggaccgccctagtaca tgtgagcaagtaccgtgttgctggagagctgcgacg aaacatcatactgattagagatcctctacgattcggtaagccta gaatatcccttcctaagcggtcaagccatagaaata aggccgccccccgctggcgggggtcccgtcgggaccccgcaacg tcccctcctcccaggcccttgaggacagccggccgg Query -Intron---> VYHSLFWPLEFTVPNRDNNKCYSKIICNKLDN <---Intron---> DRVIGFHYLGPNAGEVTQGYGAAMKCGLTKEQLDNTIGIH 114bp > |||||||||||||| |||||||/||||||||| < 82bp > ||||||||||||||||||||| ||||| ||||||/||||| Target VYHSLFWPLEFTVPGRDNNKCYAKIICNKLDN DRVIGFHYLGPNAGEVTQGYGVAMKCGATKEQLDHTIGIH gtcacttccgtagcgagaaattgaaataacga gcgagtctcgcaggggacgtgggaatggaagccgcaagac taagttgctatctcggaaaagacattgaataa agttgtaatgcacgatcagagtctaggccaaataactgta gcctgcgcggccgccacccgcccgccctagcc caccgcccggatcaggggcccacgaccccggggccccccc Query PTCAE <---Intron---> IFTTMEVTKSSGGDITQAGCUG ||||| < 1854bp > /|||||||||||||| |||||| Target PTCAE VFTTMEVTKSSGGDIKQAGCUG catgg gtaaaggaaatgggaacggttg ccgca ttcctatcagcggataacgggg acttg cccggggcgcccaccagcccat * Sequence until next stop: TAA * Distance CDS-SECIS: 315 ; UGA-SECIS: 318 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = JACSYO010000324.1:subseq_0,100000_ Strand = + Positions = 25737 - 25817 Found by: Infernal (score=27.89) Covels (score=17.73) Stem2 length = 11 Apical loop length = 18 Insertion in stem2 = 0, 0 Free Energy = -17.07 ..(((((((.......(((((((((((((((....................)))))))))))))))..........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-----cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc .({([{(((---(...{[[{((((({((((((..................))))))})))))}]]}......-..))))}])}). target UUUUGGCUG---UUUGUGACGUCCUGGCCCAUAACCUGGAAAUUACUGAGGUGGGCGAGGAUCGAUGUCCCU-CUGCAGGAGCAC **** ^^ 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