_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 5e-25 Query name: gi|27807131|ref|NP_777051.1| thioredoxin reductase 2, mitochondrial precursor [Bos taurus] >gi|190359067|sp|Q9N2I8.2|TRXR2_BOVIN RecName: Full=Thioredoxin reductase 2, mitochondrial; AltName: Full=Thioredoxin reductase TR3; Flags: Precursor >gi|5360756|dbj|BAA82153.1| thioredoxin reductase [Bos taurus] Query range: 4-511 (total 511) Target: /data/www-rg/seblastian_results/741499251/tempfiles/temptarget.fasta Chromosome: NW_018335521.1:subseq_1154754,81546_ Strand: - Positions: -Exon 1 64827 64884 -Exon 2 54847 54915 -Exon 3 51637 51693 -Exon 4 51356 51497 -Exon 5 50924 50998 -Exon 6 50203 50281 -Exon 7 49749 49811 -Exon 8 48780 48850 -Exon 9 41894 41913 -Exon 10 41206 41297 -Exon 11 39876 40050 -Exon 12 33729 33865 -Exon 13 32556 32651 -Exon 14 32284 32376 -Exon 15 30980 31051 -Exon 16 30816 30913 -Exon 17 30000 30126 Redox box: no Query LRGAAARFRGRAPGGARGAA <---Intron---> GRQCYDLLVIGGGSGGLACAKEA <---Intron---> AQLGKKVAVLDYVEPSPQG <---I ||| || | | | | < 9911bp > ||||||||||||||||||||||| < 3153bp > |||||||||||||||||/| < 1 Target LRGEGRGFRAGPPATAEGRA GRQCYDLLVIGGGSGGLACAKEA AQLGKKVAVLDYVEPSPRG ccgggcgtaggccgagggcg gccttgccgagggtggtgtgagg gccgaagggcgtggctccg tggagggtgcgcccccagg cggagaattttgggcggtcgcaa ccatgaatcttaatacccg ggcgggccgggtaatggga aggaccccggtctacccgctcga ccggggggcggccggtcca Query ntron---> TRWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAPHYGWGVAQAPHSW <---Intron---> ATLADAVQNHVKSLNWGHRIQLQDR < 39bp > |||||||||||||||||||||||||||||||||||||| |||||| | < 357bp > ||/||||||||/|||||||/||||| < Target TRWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAPHYGWAVAQAPHDW ATMADAVQNHVRSLNWGHRVQLQDR aatgcggatgaggtacaacaccggccggaacggcctgtgggcgccgt gaaggggcacgatcatgccgcccga gcgggtggcgtatggtcaattaaccttggttgaccaaggctcaccaag cctcactaaatgctaggagtataag ccggccctccactccccggggtggggggcgcctccctcgcgcgcatc ggggacctgccggcgcgccccgggc Query ---Intron---> KVKYFNVKASFVDTHTVCGVSKGGEE <---Intron---> TLLSAEHIVIATGGRPRYPTH <---Intron---> IEGALEY 642bp > ||||||/|||||/ |||||||||||| < 391bp > ||||||||||||||||||||| < 898bp > ||||||| Target KVKYFNIKASFVNAHTVCGVSKGGEE TLLSAEHIVIATGGRPRYPTH IEGALEY agattaaagatgagcagtggtagggg acctggcagagaggccctcac agggtgt ataatatacgttacactggtcaggaa cttccaatttccgggcgacca tagctaa gacgttccgcctctgcatttccatggg tgtgcgccccccaggggctac tatcgac Query GITSDDLFWLKESPGKT <---Intron---> LVVGASY <---Intron---> VALECAGLLTGLGLDTTVMIRSVPLRAFDQ <---Intron--- ||||||||||||||||| < 6866bp > ||||||| < 596bp > |||||||||||||||||||||||||||||| < 1155bp Target GITSDDLFWLKESPGKT LVVGASY VALECAGLLTGLGLDTTVMIRSVPLRAFDQ gaaaggcttcagtcgaa tggggat ggcgtggccagcgtgaagaacagcccgtgc gtcgaattgtaaccgac tttgcg atctagcgttcgtgtacctttggtctgctaa gcactcccgggactaa gggcacc cgcggtaccccgccgtcccgaccgccgcccg Query > QMASLVTEHMAGHGTRILRGCAPEKVEKLPGQQLRVTWVDLTSDRKDAGTFDTVLWAIG <---Intron---> RVPETASLNLEKAGVHTNPVTGK > ||||||||||| ||||/|||||||/||||| |||||||||| |||/| ||||||||||| < 6010bp > |||||/||||||||||||||||| Target QMASLVTEHMASHGTRVLRGCAPERVEKLPDQQLRVTWVDLASDRRDVGTFDTVLWAIG RVPETSSLNLEKAGVHTNPVTGK cagtcgagcagacgacgccgtgcgaggaccgccccgatggcgtgaagggatgagctgag cgcgatacatgagggcaacgaga atccttcaatcgagcgttgggccagtaatcaaatgtcgtatccaggatgctacttgct ggtcaccgtataacgtacactcga agtagctgcgcccccgcggctctgggagcacgactccggctcgcggcgcctccgcgca cataacatgtgggttgtaccctgg Query ILVDAQETTSVPHIYAIGDVAE <---Intron---> GRPELTPTAIMAGRLLAQRLSGRTSDLMDYSS <---Intron---> VPTTVFTPLEYGCV ||||||| |||||||||||||| < 1077bp > |||||||||||||||||||||||||||||| / < 179bp > |||||||||||||| Target ILVDAQEATSVPHIYAIGDVAE GRPELTPTAIMAGRLLAQRLSGRTSDLMDYDN VPTTVFTPLEYGCV acgggcggatgccatgaggggg gccgcacagaaggaccgcccagcatgcagtga gcaagtaccgtgtg tttacaaccctcatactgatca ggcatccccttcggttcagtgggccattaaaa tcccttcctaaggt ctttcgacctcccccccccgag ggggggcgccgcggcgcgggccgcacggcccc ccgcccccggtccg Query GLSEEAAVARHGEEHVE <---Intron---> VYHAFYKPLEFTVPQRDASQCYIK <---Intron---> MVCLREPPQLVLGLHFLGPNAGEVIQG ||||| ||||||||||| < 1232bp > |||||||||||||||||||||||| < 66bp > |||||||||||||||||||||||| || Target GLSEEVAVARHGEEHVE VYHAFYKPLEFTVPQRDASQCYIK MVCLREPPQLVLGLHFLGPNAGEVTQG gctggggggccgggcgg gtcgttaccgtagcccggtcttaa agtccgccccgcgcctcgcaggggacg gtcaatctcgagaaata taactaactatctcagaccagata ttgtgaccatttgtattgcacgatcag ggagggtgtctcggcgg tccgctgaagcgccggtatgccag ggtgggctggggcgcctcccacattga Query FALGIK <---Intron---> CGASYQQLMRTVGIHPTCAEEVAKLRISKRSGLDPTVTGCUG |||||| < 689bp > | ||| |/|||||||||||||||||||||||||||||||||| Target FALGIK CRASYLQVMRTVGIHPTCAEEVAKLRISKRSGLDPTVTGCUG tgcgaa tagttccgacaggaccatgggggaccatactgcgcagagttg tctgta ggccatattgctgtaccgcaatcatgtcagcgtacctcgggg tcggc gtgcccgggggagccccctggggcgccccgcccgccagcccac * Sequence until next stop: TAG * Distance CDS-SECIS: 885 ; UGA-SECIS: 888 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = NW_018335521.1:subseq_1154754,81546_ Strand = - Positions = 29114 - 29046 Found by: Infernal (score=31.41) Covels (score=34.51) Stem2 length = 9 Apical loop length = 14 Insertion in stem2 = 0, 0 Free Energy = -19.94 ..(((((((.......(((((((((((((((...............)))))))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc ...((((((---....([[(((({(({((((.....-.........))))}))}))))]])----..-.))))))... target CCCUGCCAG---AUGAUGAGGACCUGUGCGGAAACC-CCCUGCGGGCUGCCCAUGUCUGAG----CC-CCUGGCAUUA **** ^^^ ****