_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 5e-04 Query name: gi|385648265|ref|NP_001245307.1| thioredoxin reductase 3 [Taeniopygia guttata] Query range: 47-607 (total 607) Target: /data/www-rg/seblastian_results/862659532/tempfiles/temptarget.fasta Chromosome: CEMB01011310.1 Strand: + Positions: -Exon 1 10945 11103 -Exon 2 12947 13066 -Exon 3 14413 14485 -Exon 4 16455 16574 -Exon 5 17021 17163 -Exon 6 19739 19854 -Exon 7 21674 21899 -Exon 8 22318 22410 -Exon 9 22696 22772 -Exon 10 24795 24951 -Exon 11 28854 28961 -Exon 12 29641 29736 -Exon 13 31146 31280 -Exon 14 33641 33706 Redox box: no Query FNSLHVEYYALELDVIDDGASIQQVLAELTNQRTVPNVFVNGTHIGGCDATFQ <---Intron---> AYKDGSLQKLLGDN--QITEPYEYDLIIIGG || | /| |/| |||/|||| | |/|||||||||||/|||| ||| < 1843bp > || | |||||||/ / | |/||||/||| Target FNECHDKYSFFTFFSPDEGPSIQEVLAEFTGQKTVPNVFVNGTHVGGCDQTFQ AYHSGLLQKLLGDSKGEELEAYDYDLIVIGG tagtcgatattatttcgggcaacggtggtagcaagcagtgagacgggtgcatc gtcagttcactggaagggtggtgtgcagagg taagaaaagttcttccaagcgtaattcatcgaactcatttagcatgggaacta caaggttaattgagagaatacaaaattttgg ctatttatcttttttatatctcgaaaaacgcagtcctgtataatgtatcgttg cctccgaggtagccataggaccttcattttt Query GSGGLACSK <---Intron---> EAAALGKKVMVLDYVVPTPLGTSWG <---Intron---> LGGTCVNVGCIPKKLMHQAALLGQALQDSRKYGW |||||/||| < 1346bp > ||| ||||||||||||||||||/|| < 1969bp > |||||||||||||||||||||||||||||||/|| Target GSGGLSCSK EAATLGKKVMVLDYVVPTPLGTTWG LGGTCVNVGCIPKKLMHQAALLGQALQDSRKFGW gtggcttta gggatgaagagcgtggcactgaatg cggatgaggtacaacaccggctgcgtcgtaatgt gcggtcgca accctgaattttaattccctgccg gtggcgtatggtcaattaaccttgactaacgatgg tttacactg atcgaggacggacttataagctag attcttattccttggggtaactacgagataggtcg Query QYEEQV <---Intron---> KHNWETMVEAIQNYIGSLNWGYRVSLREKSVTYLNSYGEFVEPHKIK <---Intron---> ATNRKGQVTYHTAET /|/||| < 446bp > ||||/|||||||||||||||||||/||||/|||||/| ||/ ||||| < 2575bp > ||||||| |//||// Target EYDEQV KHNWQTMVEAIQNYIGSLNWGYRVALREKTVTYLNAYAEFIGPHKIK ATNRKGQETFYTAQS gtggcg acatcaagggacatagttatgtcggtcgaagatcagtggtagccaaa gaaaagcgattagct aaaaa taaagacttactaaatgctaggagtctgaactcatacacattgcaata ccagagaactaccac attga taccggggtaaagttaatgcgttggcgtaatgacctccagttgtcgtg attaagaatccatga Query FVVATGERPRYLGIPGDKEFCITS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQEMAEKVGAYM ||/||||||||||||||||/|||| < 1819bp > ||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||| Target FVIATGERPRYLGIPGDKEYCITS DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQEMAEKAGAYM tgagaggaccttgacggagttaaa ggcttccttcgaatggggttggcgtggtcggcgtggagagctacccgtgcgaggagggta tttccgagcgatgtcgaaaagtcg aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaacgcat tttcaaaatatataaataactta tccccagctctggtgtgaattatgataattgtttgcttcgactctctcttaagcaaatatg Query ETHGVKFIRKFVPVQ <---Intron---> VEQLEQGMPGRLKVTAKSTEGPETLEEEYNT <---Intron---> VLLAVGRDACTRNIGLQTIGVK | |||||||/|||// < 418bp > | /|| ||||||/| ||/| | | /| |||| < 285bp > ||/|/||||||/||||/ |||/ Target ENHGVKFIRQFVPIE VVKLEDGMPGRLRVIAKATGGSEMIEGEYNT VLIAIGRDACTKNIGLEKIGVQ gacggataactgcag ggatgggacgacagagagaggtgaagggtaa gtagagcggtaaaagtgaaggc aaagtattgattcta ttataagtcggtgttcaccggcattagaaac tttctggacgcaatgtaatgta acttaactggttctg tagggtcgtaacagaaaagaaaagtaaactt tgattttctttactcggattgg Query INEK <---Intron---> NGKVPVNDEERTNVPYVYAIGDILDGKLELTPVAIQAGRLLAQRLYGGSSKK <---Intron---> CDYINVPTTVFT |||| < 2022bp > |||/| ||||/|||||||||||/|/|| ||||||||||/|||/||/|||| | < 3902bp > |||||||||||| Target INEK NGKIPANDEEQTNVPYVYAIGDVLEGKPELTPVAIQAGKLLARRLFGGSSIK CDYINVPTTVFT aaga agaacgagggcaagctgtgagggtggacgcacggacggactgcactggataa tgtaagcaagta taaa agatccaaaaacatcatactgattagacatcctctacgattcggttgggcta gaatatcccttc tta gtgaatgttaagctgtcctttattaaagtattattagacgaaacgttagcccg tccatgatagca Query PLEYGSCGYPEEKAISEYGEQNLE <---Intron---> VYHTLFWPLEWTVPGRDNNTCYAKIICNKQDN <---Intron---> NRVIGLHVLGPN ||||| || ||/|/ //|/ |/| < 679bp > ||||||||||||/| ||||| |||/|||| || < 1409bp > |||/|||||||| Target PLEYGCCGLSEEQALEQFGQDNIE VYHTLFWPLEWTIPNRDNNTSYAKVICNKLDN NRVLGLHVLGPN ccgtgttgttggcgtgctgcgaag gtcatttccgtaacaagaaattgagataacga acgtgccgcgca ctaaggggtcaaactaatgaaata taacttgctagctcagaaaccacattgaataa agttgtattgca tgatcttgaaaaacaaataaccag atttgtgatagaactacctattaaacccatct cttatttttatt Query AGEVTQGFAAAIKCGLTKELLDETIGIHPTCAE <---Intron---> VFTTMDITKSSGQDITQKGCUG |||/|||| ||/|||||||||/||||||||||| < 2360bp > |||||||||/||/|||| |||| Target AGEITQGFGAAMKCGLTKELLNETIGIHPTCAE VFTTMDITKASGKDITQSGCUG gggaacgtgggaatgcaagtcagaagaccatgg gtaaagaaagtgagaactgttg cgatcagtgcctaggtcaattaactgtaccgca ttcctatcaccgaatcacgggg taatcattgaagattcagaactatctatattag tctagttagtaaatctgtccat * Sequence until next stop: TAA * Distance CDS-SECIS: 213 ; UGA-SECIS: 216 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = CEMB01011310.1 Strand = + Positions = 33920 - 33995 Found by: Infernal (score=24.35) Covels (score=21.56) Stem2 length = 9 Apical loop length = 18 Insertion in stem2 = 0, 0 Free Energy = -15.97 ..(((((((.........(((((((((((((((................)))))))))))))))........))))))).. model uucggucaugcg--UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc .((({({(((((......{[[{((({((((((..................))))))})))}]]}----))-)))})}))). target GGCACGCAAGUGUCUUUUUGAAGUUUUGGCUCUGAACCCCAUCUGGAGGCGAGUCAUAACAGAU----UA-CUUCUAUGCA **** ^^ ****