_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:QUE_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 3e-56 Query name: gi|385648265|ref|NP_001245307.1| thioredoxin reductase 3 [Taeniopygia guttata] Query range: 2-607 (total 607) Target: /data/www-rg/seblastian_results/909122223/tempfiles/temptarget.fasta Chromosome: CM003722.1:subseq_10154350,116132_ Strand: + Positions: -Exon 1 49997 50119 -Exon 2 55526 55586 -Exon 3 57160 57269 -Exon 4 57440 57553 -Exon 5 59348 59420 -Exon 6 60264 60383 -Exon 7 60771 60913 -Exon 8 62301 62416 -Exon 9 62524 62749 -Exon 10 63001 63093 -Exon 11 63535 63611 -Exon 12 64161 64317 -Exon 13 64520 64627 -Exon 14 65511 65606 -Exon 15 65813 65947 -Exon 16 66079 66144 Redox box: no Query PPPPGQTRLPDWDGLKLRVRTLIASHRVMIFSKSYCPYCNK <---Intron---> VKELFNSLHVEYYALELDVID <---Intron---> DGASIQ |||||||||||||||||||||||||||||||||/||||||| < 5406bp > ||||| |/ ||||||||| | < 1573bp > |||||| Target PPPPGQTRLPDWDGLKLRVRTLIASHRVMIFSKNYCPYCNK VKELFRSIGVEYYALELDATD DGASIQ ccccgcacccgtggcaccgcacagtccgaataaattcttaa gagctctagggttgcgcggag gggaac ccccgacgtcagagtatgtgcttccagttttgaaagcagaa taattgctgtaaactatacc aagcgta ggggagcgcgcgcgggccggtcccccccgcccgccctcccg ggaccccctggctcgagtat ttacttg Query QVLAELTNQRTVPNVFVNGTHIGGCDATFQ <---Intron---> AYKDGSLQKLLGDNQITEPYEYDLIIIGGGSGGLACSK <---Intron---> ||| ||||||||||||||||||||||||/| < 170bp > ||/||||||||||||||||||||||||||||||||||| < 1794bp > Target QVLVELTNQRTVPNVFVNGTHIGGCDATYQ AYQDGSLQKLLGDNQITEPYEYDLIIIGGGSGGLACSK cgtggcaacaagcagtgagacaggtggatc gtcggtccaccggacaagctgtgcaaagggtggcgtta atttatcaagctcatttagcatgggaccaa caaagctaattgaaatcacaaaattttgggcggtcgca aagaggccggagttatgtatcttcttagtg ttgtaaggactgccataactattctttttcatatattg Query EAAALGKKVMVLDYVVPTPLGTSWG <---Intron---> LGGTCVNVGCIPKKLMHQAALLGQALQDSRKYGWQYEEQV <---Intron---> KHN ||| ||||||||||||||||||||| < 843bp > |||||||||||||||||||||||||||||||||||||||| < 387bp > ||| Target EAATLGKKVMVLDYVVPTPLGTSWG LGGTCVNVGCIPKKLMHQAALLGQALQDSRKYGWQYEEQV KHN gggatgaagagtgtggcaccgattg cggatgaggtacaacaccggccgcgccgtaatgtctggcg aca accctgaattttaattccctgccg gtggcgtatggtcaattaaccttgactaacgaaggaaaaa taaa attcgggaagaattttaattacag attcgtatatcttggggtaaatgtgacgtaggtgggtaaa tacc Query WETMVEAIQNYIGSLNWGYRVSLREKSVTYLNSYGEFVEPHKIK <---Intron---> ATNRKGQVTYHTAETFVVATGERPRYLGIPGDKEFCITS || ||||||||||||||||||||||||||||||||||||||||| < 1387bp > |||||||||||||||||/||||||||||||||||||||| Target WEIMVEAIQNYIGSLNWGYRVSLREKSVTYLNSYGEFVEPHKIK ATNRKGQVTYHTAETFVLATGERPRYLGIPGDKEFCITS tgaagggacatagttatgtcgtcagatgatcattggtggccaaa gaaaagcgatcaggatgcgaggacatcgacggagttaaa gatttactaaatgctaggagtctgaactcatacagattacaata ccagagatcaaccactttccgagcgatgtcgaaatgtcg gacgaaatgcctttacgatagcgaggtgacctttcgtgaacatg atcaaaaactcaagttcgaaaagaacgtctataaccta Query <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQEMAEKVGAYMETHGVKFIRKFVPVQ <---Intro < 107bp > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 251bp Target DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQEMAEKVGAYMETHGVKFIRKFVPVQ ggcttccttcgaacggggttggcgtggtcggcgcggagagctacccgtgcgaggagggtagacggataaatgcgc aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgcatacagtattgattcta ttcgccgtcctcgtgtgttttatggtagtgtcgtgtcagggtcctggttcgagaaactccgagctggtcgatattg Query n---> VEQLEQGMPGRLKVTAKSTEGPETLEEEYNT <---Intron---> VLLAVGRDACTRNIGLQTIGVKINEK <---Intron---> NGKVP > ||||||||||||||||||||| | ||||| < 441bp > ||||/||||||||||||||||||||| < 549bp > ||||| Target VEQLEQGMPGRLKVTAKSTEGSEIFAEEYNT VLLAIGRDACTRNIGLQTIGVKINEK NGKVP ggccgcgacgacagagataggtgatgggtaa gttgagcggtaaaagtcaaggaaaga agagc taataagtcggtatccaccagcattcaaaac tttctggacgcgatgtactgtataaa agatc tggagaagaaagagaagttgaaactaaatct tgacttttatcgtttagactcactg gtgact Query VNDEERTNVPYVYAIGDILDGKLELTPVAIQAGRLLAQRLYGGSSKK <---Intron---> CDYINVPTTVFTPLEYGSCGYPEEKAISEYGEQNLE |||||/|||||||||||||||||||||||||||||||||||||||/| < 202bp > ||||||||||||||||||||||||||/ |||/|||| Target VNDEEQTNVPYVYAIGDILDGKLELTPVAIQAGRLLAQRLYGGSSRK CDYINVPTTVFTPLEYGSCGYPEEKAMEEYGKQNLE gagggcaagctgtgaggatggacgcacggacggaccgcactggataa tgtaagcaagtactgtgatgtcggagaggtgacatg taaaaacatcatactgattagatatcctctacggttcagtagggcga gaatatcccttcctaaggggacaaactaaagaaata attaaaccgttttatgtcgtagtattatctgagaggcaggtgttcag tctctaaaagtctagtcctgttaaacgaatggacgg Query <---Intron---> VYHTLFWPLEWTVPGRDNNTCYAKIICNKQDN <---Intron---> NRVIGLHVLGPNAGEVTQGFAAAIKCGLTKELLDETI < 883bp > ||||||||||||| |||||||||||||||||| < 206bp > ||||||||||||||||||||||||||||||||||||| Target VYHTLFWPLEWTVAGRDNNTCYAKIICNKQDN NRVIGLHVLGPNAGEVTQGFAAAIKCGLTKELLDETI gtcatttccgtagggagaaattgaaataacga acgagccgcgcaggggacgtgggaatgcaagtcggaa taacttgctagctcggaaacgacattgaaaaa agttgtattgcacgatcagtccctaggtcaattaact ttctacgatagagacatctcttagtcctagct ttgaggtttactttatcattttacgttccaaattaat Query GIHPTCAE <---Intron---> VFTTMDITKSSGQDITQKGCUG |||||||| < 131bp > |||||||||||||||||||||| Target GIHPTCAE VFTTMDITKSSGQDITQKGCUG gaccatgg gtaaagaaattgcgaacagttg gtaccgca ttcctatcaccgaatcaagggg tctcttag actagttcattaacctggccat * Sequence until next stop: TAA * Distance CDS-SECIS: 215 ; UGA-SECIS: 218 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = CM003722.1:subseq_10154350,116132_ Strand = + Positions = 66360 - 66452 Found by: Infernal (score=29.64) Covels (score=25.0) Stem2 length = 11 Apical loop length = 16 Insertion in stem2 = 0, 0 Free Energy = -28.39 ..(((((((.......................(((((((((((((((................)))))))))))))))........))))))).. model uucggucaugcg----------------UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc ((((((((((((....................{[[{(((((((((((................)))))))))))}]]}..--.)))))))))))) target CUUUGCUUGGCAUUAGCACUGCGGUGCUUCUUUGACGUUGUAGCUCAGAACCUUCUCACCAGGUGAGCUACGACUGAUGG--CUGCCAGGCAAGG **** ^^ ****