_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 4e-28 Query name: gi|315138999|ref|NP_001186707.1| selenoprotein N precursor [Taeniopygia guttata] Query range: 1-533 (total 533) Target: /data/www-rg/seblastian_results/811461335/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: + Positions: -Exon 1 47173 47286 -Exon 2 50006 50123 -Exon 3 51130 51260 -Exon 4 51696 51908 -Exon 5 52557 52681 -Exon 6 53393 53530 -Exon 7 54323 54404 -Exon 8 55319 55507 -Exon 9 56410 56515 -Exon 10 57578 57690 -Exon 11 58341 58442 -Exon 12 59240 59407 Redox box: no Query MAGPGPGAAPPRLALALALLAVLLAIKYYRDAEAARQQ <---Intron---> ELALKSLGNEGLFLFSSLDTNKDLYLSPEEFKPIAEKLTG <---I ||||||||||||||||||||| |/|/|||||||||||| < 2719bp > |||||||||||||||||||||||||||||||||||||||| < 1 Target MAGPGPGAAPPRLALALALLAALVAVKYYRDAEAARQQ ELALKSLGNEGLFLFSSLDTNKDLYLSPEEFKPIAEKLTG aggcgcgggccccgcgcgccggcgggattcgggggccc gcgcattgaggctctttcgaaagctcacggtacaggacag tcgcgcgccccgtctctcttccttctaaagacaccgaa atctactgaagttttcctacaaatatgcaatactcaatc gggggcggctgcgggcgcgccgggccgccgcggggggg ggtggcggtgggcccccgcccgcgcgcaggcacttggca Query ntron---> VPAVSESEEEETPDPDGETLSIVAKFQPLLMETMTKSKDGFLG <---Intron---> ISHVALSGLRNWTAPAAPMSVLLARQFKAFL 006bp > | |||||||| |||||||||||||||||||||||||||||| < 435bp > ||||||||||||||||||||||||||||||| Target VAPASESEEEETLDPDGETLSIVAKFQPLLMETMTKSKDGFLG ISHVALSGLRNWTAPAAPMSVLLARQFKAFL ggcgtgtggggacgcgggattaggatcctcagaaaaaaggttg atcggctgcaatagcggcaagccgactagtc gtccccacaaaactacagactcttcatactttactcagaagttg tcatctcgtgagcccccctgtttcgatactt gttacaatagggggtacggtgccgcacgcgcgaagggcgttcga tccgtgtgcgcgacaactgtcgtcggcactc Query PPKDNLDLGDPWWIIPSELNIFTGYLSNNRFYPPPPKGKE <---Intron---> VIIHKLLSMFHPRPFVRTRFAPQGAVACIQASSSFYYTIAFR < |||||||||||||||||||||||||||||||||||||||| < 648bp > ||||||||||||||||/||||||||||||||||||||||||| < Target PPKDNLDLGDPWWIIPSELNIFTGYLSNNRFYPPPPKGKE VIIHKLLSMFHPRPFVKTRFAPQGAVACIQASSSFYYTIAFR ccagacgcggcttaacagcaatagtctaaattccccagag gaacaccaatcccctgaactgccggggtacgaaatttaagtc ccaaatatgacggttcgatattcgatcaagtaccccagaa tttaattgttacgcttacgtccagctcgtacgggtaactctg tagttgttgtgggatctagccctctccccgtctatcgcag gcccgggcgccggcccggcccggacgcccgccccccccacc Query ---Intron---> IHAEFQLNEPPNFPFWFSPGQFTGYIVLSKDSSHIRDFRLFVPNNR <---Intron---> SLNVDMEWLYGASESSNMEVDIGY 711bp > |||||||||||/||||||||||||||||||||||/||||||||||| < 792bp > |||||||||||||||||||||||| Target IHAEFQLNEPPDFPFWFSPGQFTGYIVLSKDSSHVRDFRLFVPNNR SLNVDMEWLYGASESSNMEVDIGY acggtccagccgtcttttcgctagtagctagttcgagtactgcaaa tcaggagtctggagaaaagggagt tacatataaccatctgtccgatcgatttcaaccatgatgtttcaag ctatatagtagcgaggatatatga gcctacggcgaaccccgtcgggcatctcgcgctcccgccgctttcc gcgcgcggggtgctgcccgagctac Query LPQ <---Intron---> MELESTGPSVPTVIHDENGNVLDSRDPSGEPIQFVFEEITWQQEIPWQEAAHRLEVAMYPFKK <---Intron---> IS ||| < 914bp > ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| < 902bp > || Target LPQ MELESTGPSVPTVIHDENGKVLDSRDPSGEPIQFVFEEITWQQEIPWQEAAHRLEVAMYPFKK IS ccc agcgtagctgcagacggagagcgaagctggcactgtggaatccgactcgggcacgggatctaa at tca tataccgcctccttaaaagattaggaccgactatttaatcgaaatcgaaccagtatctactaa tc gtg gggacagcggccgcctgcggcgccgccaggccgtgtggccggggccgggaccggggcgtatgg cc Query YLPFTEAFERAQAEKKLVHSILLWGALDDQSCUG <---Intron---> SGRTLRETVLESSPILALLNESFISSWSLVKELEELQ <---Intron-- |||||||||||||||||||||||||||||||||| < 1062bp > ||||||||||||||||||||||||||||||||||||| < 650bp Target YLPFTEAFERAQAEKKLVHSILLWGALDDQSCUG SGRTLRETVLESSPILALLNESFISSWSLVKELEELQ tcctaggtgagcggaacgctacctggcggctttg tgcaccgagcgatcacgccagataaattcgagcggcc atctcactagcacaaattactttggctaaacgg gcggctgacttagccttcttaagttgggcttaataata cgccaactgaaaagggggcccgcgtcgtcgcca tggatcggccgatgccccggcgcccccgcggggggggg * Query -> SNRENEFYSKLAKLHLEKYNFPVEMIICLPNGTV <---Intron---> IHHINANYFLDITSMKPEDVESSIFSFSTNFEDPSTATYLQFLKEGL > ||||||||||||||||||||||||||/||||||| < 797bp > ||||||||||||||||||||||||||||||||||||||||||||||| Target SNRENEFYSKLAKLHLEKYNFPVEMILCLPNGTV IHHINANYFLDITSMKPEDVESSIFSFSTNFEDPSTATYLQFLKEGL aaagagttaacgacccgatatcggaactccagag accaagattcgaataacggggaaatattaatggctagatcctcaggc gagaaatagatcatataaaatctatttgtcagct taatacaattatcctacaataggttgtccataacccccatattaagt ccagtgcccaacggcggaccctgggcccccccgg tccctcctcgctttggtattacccttcacttactaaatccgcggagg Query HRAKPYLQP ||||||||| Target HRAKPYLQP cagactccc agcacatac caaaacggc Sequence until next stop: TAA * Distance CDS-SECIS: 1910 ; UGA-SECIS: 2294 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = your_sequence Strand = + Positions = 61318 - 61388 Found by: Infernal (score=24.53) Covels (score=28.39) Stem2 length = 10 Apical loop length = 10 Insertion in stem2 = 0, 0 Free Energy = -37.42 ..(((((((.......(((((((((((((((...............)))))))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc (((((((((.......{[[{(((({((((((........-----..))))))}))))}]]}..--....))))))))) target UCCCUCCCGUGCCUGGUGACGCCCUGGCCCGAAACCCGC-----GGCGGGCCCGGGCCGAUGU--CGGCCGGGAGGGG **** ^^^ ****