_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 9e-22 Query name: gi|5107031|gb|AAD39929.1|AF133519_1 thioredoxin reductase 3, partial [Homo sapiens] Query range: 14-577 (total 577) Target: /data/www-rg/seblastian_results/589770392/tempfiles/temptarget.fasta Chromosome: QVIC01000475.1: Strand: + Positions: -Exon 1 48267 48333 -Exon 2 50004 50113 -Exon 3 52514 52618 -Exon 4 52901 52973 -Exon 5 54090 54209 -Exon 6 55925 56067 -Exon 7 57131 57246 -Exon 8 59426 59651 -Exon 9 60717 60809 -Exon 10 66746 66822 -Exon 11 67676 67832 -Exon 12 74322 74429 -Exon 13 77347 77442 -Exon 14 78424 78558 -Exon 15 78936 79001 Redox box: no Query TRVKELFSSLGVECNVLELDQVD <---Intron---> DGARVQEVLSEITNQKTVPNIFVNKVHVGGCDQTFQ <---Intron---> AYQSGLLQK /||||||||||/||/||||||| < 1670bp > || ||||/|/||||||||||||||/|||||||/||| < 2400bp > |/ |||||| Target XQVKELFSSLGVDCNILELDQVD DGIRVQEMLTEITNQKTVPNIFVNRVHVGGCDRTFQ AHHSGLLQK tcgagctttcgggtaatgcgcgg ggacgcgacagaaacaagcaatgaagcgggtgaatc gccagctca tataattcctgtagattataat aagtgtaattcatcaaactcatttagtatgggagcta caaggttaa nggaactttgagctccgattac ttgcttaaggaacttggggccttgtagcgaatcgtcg atccggagg Query LLQEDLAYDYDLIIIGGGSGGLSCAK <---Intron---> EAAILGKKVMVLDFVVPSPQGTSWG <---Intron---> LGGTCVNVGCIPKKLMH |||| | |||||/|||||||||||| < 282bp > |||||||||/||||||||||||||| < 1116bp > ||||||||||||||||| Target LLQEGSANDYDLIVIGGGSGGLSCAK EAAILGKKVLVLDFVVPSPQGTSWG LGGTCVNVGCIPKKLMH cccggtgagtgcagagggtggcttga gggatgaagcgcgtggctccgattg cggatgaggtacaacac ttaagccaaaattttgggcggtcgca accttgaattttatttcccagccg gtggcgtatggtcaatta cggacgcttttctcttttttccgtag aactgagacgcgctgctctgcacg ctacttgttctttgaggc Query QAALLGQALCDSRKFGWEYNQQV <---Intron---> RHNWETMTKAIQNHISSLNWGYRLSLREKAVAYVNSYGEFVEHHKIK <---Intron--- ||||||||| ||/|||||||||| < 1715bp > /||| |/|/|/|||| |||| |||||||| | |||/|||||/||||| < 1063bp Target QAALLGQALQDSKKFGWEYNQQV KHNWSTLTEAVQNHIGSLNWSYRLSLREKGVTYVNAYGEFVDHHKIK cggccgcgtcgtaatgtgtaccg acataacagggcacagtcatatattcagaggatgagtggtggccaaa accttgactaacaatggaaaaa taaaggctcactaaatgctaggagtctgaagtcatacagattaaaata ggctaagcggcagatcggttag ggccgccgagctgcccctccgccgggggggagccctccgatgcttacg Query > ATNKKGQETYYTAAQFVIATGERPRYLGIQGDKEYCITS <---Intron---> DDLFSLPYCPGKPLVVGASYVALECAGFLAGFGLDVTVMVRSI > ||||||||/|//|//|||||||||||||||||||||||| < 2179bp > |||||||||||| |||||||||||||||||||||/|||||||| Target ATNKKGQESYFSASKFVIATGERPRYLGIQGDKEYCITS DDLFSLPYCPGKTLVVGASYVALECAGFLAGFGLEVTVMVRSI gaaaagcgatttgtatgagaggaccttgacggagttaaa ggcttccttcgaatggggttggcgtggtcggtgtggagagcta ccaaagaagatcccatttccgagcgatgtagaaaagtcg aattctcagcgactttgccatctagcgttcgtgtatctttgct actaaagatttttagtcaagtagagcgccagtaaccta tccgctgtccccgcaggtcttccggcactagctcgagcgggacc Query LLRGFDQEMAEKVGSYMEQHGVKFLRKFIPVM <---Intron---> VQQLEKGSPGKLKVLAKSTEGTETIEGVYNT <---Intron---> VLLAI ||||||||||||||||||/|||||||||/|| < 1065bp > |||||/|||||||| |||||| ||/| |||| < 5936bp > ||||| Target LLRGFDQEMAEKVGSYMERHGVKFLRKFVPVK VQQLERGSPGKLKVWAKSTEGPETMEEVYNT VLLAI cccgtgcgaggaggttagacggattaatgcga gcccgagtcgacagtgataggcgaagggtaa gccga ttggtaaatcaatgcatagagtattgattcta taataggccgatatgcaccagcactaataac tttct tttctcaggagagtccggatctgcggatctgg tggggacacaggaggtactaaaacggggcca cgact Query GRDSCTRKIGLEKIGVKINEK <---Intron---> SGKIPVNDVEQTNVPYVYAVGDILEDKPELTPVAIQSGKLLAQRLFGASLEK <---Intron ||||||||/|||||||||||| < 853bp > /|||||||/||||||/|||/||/|| ||||||||||/|||||/|||||| || < 6489bp Target GRDSCTRKLGLEKIGVKINEK NGKIPVNDMEQTNVPHVYAIGDVLEGKPELTPVAIQAGKLLARRLFGASSEK gcgttaaatgtgaaggaaaga agaacgagagcaagccgtgagggtggacgcacggacggaccgcactggttga ggacgcgatgtaatgtataaa agatctaataacatcatactgattagacatcctctacgattcggttgcccaa ctcctagaacgggttcactg gtcgcagtcgagccgccctcccccggcaaggttgccgacggatcgntgcgaaa Query ---> CDYINVPTTVFTPLEYGCCGLSEEKAIEVYKKENLE <---Intron---> IYHTLFWPLEWTVAGRENNTCYAKIICNKFDH <---Intron > |||//||| ||||||||||||||||||||||||||| < 2917bp > /|||||||||||||||/||||||||||/| | < 981bp Target CDYMSVPTAVFTPLEYGCCGLSEEKAIEVYKKENLE VYHTLFWPLEWTVAGRDNNTCYAKIICHKPDS tgtaagcaggtaccgtgttgctggagaggtaagacg gtcacttccgtagggagaaattgaaatcacga gaatgtcccttcctaaggggtcaaactataaaaata taacttgctagctcggaaacgacattgaacag tttgttaccgcatgatcctagaaaagtagtaagtaa gcctgcgtcagaaccactctttggccccatcc Query ---> DRVIGFHILGPNAGEVTQGFAAAMKCGLTKQLLDDTIGIHPTCGE <---Intron---> VFTTLEITKSSGLDITQKGCUG > |||||||||||||||/||||||||||||||||||||||||||||| < 377bp > |||||||||||||||||||||| Target DRVIGFHILGPNAGEITQGFAAAMKCGLTKQLLDDTIGIHPTCGE VFTTLEITKSSGLDITQKGCUG gcgagtcacgcagggaacgtgggaatgcaacccggaagaccatgg gtaacgaaattgcgaacagttg agttgtattgcacgatcagtccctaggtcaattaactgtaccgga ttcctatcaccgtatcaagggg tagaattttaacctgtcaacaccgatgccaaggtcccacccatgg ccatgacagaaagcccggccag * Sequence until next stop: TAG * Distance CDS-SECIS: 208 ; UGA-SECIS: 211 ------- SECIS element -- id:1 -- grade:B ---- Chromosome = QVIC01000475.1: Strand = + Positions = 79210 - 79255 Found by: Infernal (score=16.89) Covels (score=8.48) Stem2 length = 11 Apical loop length = 16 Insertion in stem2 = 0, 0 Free Energy = -16.79 ..(((((((.......(((((((((((((((................)))))))))))))))........))))))).. model uccgggcaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugcccggc ----------------{[[{(((((((((((................)))))))))))}]]}----------------- target ----------------UGACGCCCUGGCUUGGAGCCCCCUGGUGAGGUGAGCCAGGGCCGAC----------------- **** ^^ ****