________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:QUE_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 6e-21 Query name: gi|5107031|gb|AAD39929.1|AF133519_1 thioredoxin reductase 3, partial [Homo sapiens] Query range: 1-577 (total 577) Target: /data/www-rg/seblastian_results/718270637/tempfiles/temptarget.fasta Chromosome: JAHTZZ010000006.1:subseq_170153188,100284_ Strand: + Positions: -Exon 1 32460 32504 -Exon 2 39930 39990 -Exon 3 40897 41006 -Exon 4 45496 45600 -Exon 5 45806 45878 -Exon 6 46781 46900 -Exon 7 49040 49182 -Exon 8 49351 49466 -Exon 9 50053 50278 -Exon 10 50985 51077 -Exon 11 56440 56516 -Exon 12 57257 57413 -Exon 13 58023 58130 -Exon 14 61508 61603 -Exon 15 65264 65398 -Exon 16 65551 65616 Redox box: no Query RVVIFSKSYCPHSTR <---Intron---> VKELFSSLGVECNVLELDQVD <---Intron---> DGARVQEVLSEITNQKTVPNIFVNKVHVGGCD |||||||/||||||| < 7425bp > ||||||||||/|||||||||| < 906bp > /|| |||||||||||/|||/|||||||||||| Target RVVIFSKTYCPHSTR VKELFSSLGVDCNVLELDQVD EGASVQEVLSEITNQRTVPSIFVNKVHVGGCD cggataaattccaac gagctttcgggtagtgcgcgg gggagcggctgaaacaagcaatgaagcgggtg gttttgacagcagcg taattcctgtagattataat aagcgtaattcatcaagctcgtttaatatggga cgccccgcctgccgg taactttgatctccgattat tagctcggtaggcccggtgctctgtagcgcttc Query QTFQ <---Intron---> AYQSGLLQKLLQEDLAYDYDLIIIGGGSGGLSCAK <---Intron---> EAAILGKKVMVLDFVVPSPQGTSWG <-- ||| < 4489bp > | ||||||/|||/| ||||||//|||||||||||/ < 205bp > |||/||/|||||||| |||/||/|| < Target HTFQ AQQSGLLQRLLQQDPAYDYDLVVIGGGSGGLSCAQ EAAVLGRKVMVLDFVAPSPRGTAWG catc gccagctccccccgcgtgtgcggagggtggcttgc ggggcgaagagcgtggctccgagtg acta caaggttagttaaaccaaaattttgggcggtcgca accttggattttattccccggccg ctcg tggtcgaggccggtggtccccccctgccgccgttg acccagagcgggccgcaccccgcg Query -Intron---> LGGTCVNVGCIPKKLMHQAALLGQALCDSRKFGWEYNQQV <---Intron---> RHNWETMTKAIQNHISSLNWGYRLSLREKAVA 902bp > |||||||||||||||||||||||||| |/|||||||/||| < 2139bp > /|/| ||//|||/|/ ||/||/||/|||||| Target LGGTCVNVGCIPKKLMHQAALLGQALADARKFGWEYSQQV KHSWATMSEAIQSHVGSLSWGHRLALREKAVT cggatgaggtacaacaccggccgcgcgggaatgtgtaccg acatgaatggacacggtcatgcccgccgagga gtggcgtatggtcaattaaccttgactcacgatggaagaa taaggcctcactagatgctgggagtctgaactc tgtcgtgttctcgggggcgcggacgggctcggccggctga ggccgccgggccgccccggcgctggcggggagc Query YVNSYGEFVEHHKIK <---Intron---> ATNKKGQETYYTAAQFVIATGERPRYLGIQGDKEYCITS <---Intron---> DDLFSLPYCPGKPL ||||||||||||||| < 168bp > |||/|||| /||||/|||||||||||||| ||/|||||| < 586bp > ||||||||||| | Target YVNSYGEFVEHHKIK ATNEKGQEAFYTAAKFVIATGERPRYLGIPGDREYCITS DDLFSLPYCPGATL tgattggtggccaaa gaagagcggttaggatgagaggaccttgacggagttaaa ggcttccttcggac atacagattaaaata ccaaagaactacccatttccgagcgatgtcgagaagtcg aattctcagcgcct cccccggttgccacg actagagggttttcgtccgaagggccggcgacagcccc cccgcggcccgcgcg Query VVGASYVALECAGFLAGFGLDVTVMVRSILLRGFDQEMAEKVGSYMEQHGVKFLRKFIPVM <---Intron---> VQQLEKGSPGKLKVLAKSTEGTE ||||||||||||||||| ||/|||||||/||||||||||||||/ |/| ||/ ||||/|| < 706bp > ||||||| ||/|||/|||||| | Target VVGASYVALECAGFLAGLGLEVTVMVRSVLLRGFDQEMAEKVGASMQQLGVRLLRKFVPVE VQQLEKGLPGRLKVVAKSTEGIE ggggttggcgtggtcggcgcggagagctgcccgtgcgaggagggtacccggccccatgcgg gcccgagccgacagggataggag ttgccatctagcgttcgtgtatctttgctttggtaaatcaatgcctaatgtgttgattcta taataagtcggtattcaccagta ggcgccggggtgctgccgcggcgcggcggcggctcgggtgggcccgggccgccgcgtgtgg cgggggcgcggggcgtacgagag Query TIEGVYNT <---Intron---> VLLAIGRDSCTRKIGLEKIGVKINEK <---Intron---> SGKIPVNDVEQTNVPYVYAVGDILEDKPELTPVA |/|||||| < 5362bp > ||||||||| |/|/||||||| |/|| < 740bp > /||||||| |||/|||||||||/|| ||/||||| Target TMEGVYNT VLLAIGRDSRTKKLGLEKIGVNISEK TGKIPVNDEEQTSVPYVYAVGDVLEGKPQLTPVA aagggtaa gttgagcgtcaaatgcgaaggaaaga agaacgagggcaagctgtgggggcggacccacgg ctagtaac tttctggacgcaatgtaatgtatgaa cgatctaaaaacgtcatactgattagacatcctc aggcgccg tgaatttcctgggaggggctgcctg ggcgcaatcgggctgcccctcgccggcgagccgcc Query IQSGKLLAQRLFGASLEK <---Intron---> CDYINVPTTVFTPLEYGCCGLSEEKAIEVYKKENLE <---Intron---> IYHTLFWPLEWTVA ///|||||/|||| || < 609bp > |||/|||| ||||||||||| ||||| |||/ ||| < 3377bp > /||||||||||||| Target VRAGKLLARRLFGGRSEK CDYVNVPTVVFTPLEYGCCGYSEEKAGEVYQAENLN VYHTLFWPLEWTVA gcggaccgcactggctga tgtgagcaggtactgtgttgttggaggggtcggaca gtcacttccgtagg tgcgattcggttgggcaa gaatatcctttcctaaggggacaaacgataacaata taacttgctagctc gggcggggagccgcaagg tcccccccggcgcggccctgcagggtcggcgggtgt ccctgcgtcggagc Query GRENNTCYAKIICNKFDH <---Intron---> DRVIGFHILGPNAGEVTQGFAAAMKCGLTKQLLDDTIGIHPTCGE <---Intron---> VFTTL |/|/|||||||||| |/ < 3660bp > |||||||/|||||||/|||||||||||||||||| |||||||||| < 152bp > ||||| Target CRDNDTCYAKIICNKLDN DRVIGFHVLGPNAGEITQGFAAAMKCGLTKQLLDGTIGIHPTCGE VFTTL tagagattgaaataacga gcgagtcgcgcagggaacgtgggaatgcaacccggaagaccatgg gtaat ggaaacgacattgaataa agttgtattgcacgatcagtccctaggtcaattagctgtaccgga ttcct caccctccggacctagcc tggaatcccagccggctggtcccggtgcgggggtcccgcccgcag gcccg Query EITKSSGLDITQKGCUG ||||/|||||||||||| Target EITKASGLDITQKGCUG gaaagtgcgaacagttg atcaccgtatcaagggg gccgagagccggaccac * Sequence until next stop: TAG * Distance CDS-SECIS: 121 ; UGA-SECIS: 124 ------- SECIS element -- id:1 -- grade:B ---- Chromosome = JAHTZZ010000006.1:subseq_170153188,100284_ Strand = + Positions = 65738 - 65808 Found by: Infernal (score=20.73) Covels (score=14.46) Stem2 length = 10 Apical loop length = 11 Insertion in stem2 = 0, 0 Free Energy = -13.8 ..(((((((.......(((((((((((((((................))))))))))))))).........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc ...(((({(---....{[[{((((({(((((.........-----..)))))})))))}]]}.....-...)}))))... target CUUGCUGCC---UCCUUGACGUCUUUGCUCGGAGCCGCCA-----GGUGAGCCAAGACCGACCUCUG-CCCGCCAGCUCC **** ^^ ****