Seblastian output

Selenoprotein id: 1 Category: known selenoprotein

Protein prediction
Predicted by: exonerate Blastx evalue: 5e-47
Query protein: gi|658131683|emb|CCX35035.1| thioredoxin reductase 3a [Oncorhynchus mykiss]
Positions on query: 1-603 Query length: 603

Target name: JARO01000300.1:subseq_1,97159_
Positions on target: 38296-38412,40021-40081,40751-40860,41950-42057,43624-43696,43795-43914,44078-44220,44371-44486,45063-45288,45390-45482,45966-46042,46427-46583,47049-47156,47311-47406,47488-47622,47815-47880 Strand: +

  Query   MPPIDNDTGRNQLKTRIQELIDSNQVLVFSKSHCPFCVK <---Intron---> VKDLFKELNVNCNVV
          |||  /   | /|//||/ || | /|/|||||/||/| | <   1608bp   > ||/|||/|||   |/
  Target  MPPTGSGPEREELRSRIEGLIGSQRVMVFSKSYCPYCTK                VKNLFKDLNVQFGVL
          accagtgcgcggcaacaggcagtccgagtaaattcttaa                gaactagcagctggt
          tcccgcgcagaatgggtagttgcagttttgagagcagca                taattaatatatgtt
          gtatattcagggggtacgtgcggggcggctgcccgctcg                tgtccaccctgttgg


  Query   ELDLID <---Intron---> EGSNYQELLLEMTRQKTVPNVFVNKTHIGGCDKTMQA <---Intron
          ||||// <   669bp    > |||/||//| ||| ||||||||/||||/||||||||| <   1089bp
  Target  ELDLVE                EGSSYQDVLFEMTGQKTVPNVFINKTHVGGCDKTMQA
          gcgcgg                ggtatcggctgaagcaagcagtaaaacgggtgaaacg
          atatt                aagcgaaatttatcgaactcatttaacatgggaactac
          ggttg                ggtgctgtggtagcgagacatccccacccgctcgagg


  Query   ---> HKDGILQKLLCGENEVYEYDLIVIGGGSGGLACSKE <---Intron---> AATLGKKVMVLDY
             > ||||/|//||  |   |/|||||||||||||||||| <   1566bp   > || ||||||||||
  Target       HKDGLLRQLLGEEEPAYDYDLIVIGGGSGGLACSKE                AALLGKKVMVLDY
               caggctcctcggggcgtgtgcagagggtggcgttag                ggttgaagagcgt
               aaagttgattgaaaccaaaattttgggcggtcgcaa                ccttgaattttaa
              tcgtccgtgggcaaaactctcctacgacaggtcttga                aaagcggggcgcc


  Query   VVPTPKGNSWGL <---Intron---> GGTCVNVGCIPKKLMHQTALLGTSIQDARKFGWEVPEETVK
          ||||| | /||| <    98bp    > |||||||||||||||||||||||//||/| ||||  // |/
  Target  VVPTPIGTTWGL                GGTCVNVGCIPKKLMHQTALLGTALQDSRNFGWEF-DKKVE
          ggcacagaatgc                ggatgaggtacaacaccagccgagccgtcatgtgt-gaagg
          ttccctgccgg                tggcgtatggtcaattaaccttgcctaacgatggat-aaata
          gctgacaatgt                gtcatgtgcctaggcgcgacggtcggactttttggt-cgagg


  Query   <---Intron---> HNWETMKTAVNNYIGSLNWGYRVALRDKNVNYVNSYAEFIEPHKIKAT <---In
          <   163bp    > |||||||||||||| |||||||| |||||||||||||||/|||||||  <   15
  Target                 HNWETMKTAVNNYISSLNWGYRVQLRDKNVNYVNSYAEFMEPHKIKAI
                         catgaaaaggaataatcatgtagcccgaagatgattggtagccaaaga
                         aagactacctaaatgctaggagtatgaaataatacacattacaatact
                         ccggtgggtgccccccccgccggggtcgctctcctctgtggtcacac


  Query   tron---> NKRGKETFHTAAKFILATGERPRYLGIPGDKEYCITSDD <---Intron---> LFSLPH
          0bp    > |||||||||||||//|||||||||||||||||/|||||| <   576bp    > |||||/
  Target           NKRGKETFHTAAKYVLATGERPRYLGIPGDKEFCITSDD                LFSLPY
                   aacgagatcaggatgtgaggccctcgacggagttaaagg                cttcct
                   aaggaactacccaattccgagcgatgtcgaaatgtcgaa                ttctca
                  acaaaggcccaaggtgggcagtaccgtctgcggcccccc                cgccgtc


  Query   CPGKTLVIGASYVALECGGFLAGLGLDVTVMVRSILLRGFDQDMANRAGEHMEEHGVKFLRKYVPVKVEE
          |||||||/||||||||| ||||||||||||||||||||||||||||| |||||||||/||||/|| |||/
  Target  CPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQDMANRVGEHMEEHGVRFLRKFVPTKVEQ
          tcgaacggggttggcgtggtcggcgcggagagctacccgtgcgagacgggcaggcggatcaatgcaaggc
          gcgactttgccatctagcgttcgtgtatctttgctttggtaaatcagtgaataaagtgttgattccata
          cggaggggtcccgcagctccaaagggtctcggcctcctctcgcgtcttcacgggtgcgccggttctgag


  Query    <---Intron---> LEAGTPGRLKVTAKSTESDETIEGEYNTVLI <---Intron---> AVGRDAC
           <   101bp    > || |/|||||||||||| || |||||||||| <   483bp    > |||||||
  Target                  LETGSPGRLKVTAKSTEIDEAIEGEYNTVLI                AVGRDAC
                          tgagtcgatagagatagagggagggtaagta                gggcggt
                         atacgccggtatccaccataactagaaacttt                ctggacg
                         ggatgctagggcacgaaattactaagcttagt                tgccccc


  Query   TGKIGLDQAGVKVNPKNGK <---Intron---> VPVNDEEQTNVPHIYAIGDILEGKWELTPVAIQAG
          || ||||/|||||| |||| <   384bp    > /| ||||||||||||||||||||||||||||||||
  Target  TGNIGLDKAGVKVNEKNGK                IPANDEEQTNVPHIYAIGDILEGKWELTPVAIQAG
          agaagcgagggagagaaga                acgagggcaagccatgaggacggatgcacggacgg
          cgatgtaacgtataaaaga                tccaaaaacatcatactgattagagatcctctacg
          accccccattcaccggcg                gcggtcaggtcgccctccactgggggagacgtcgtg


  Query   KLLARRLYAGASLKCDYV <---Intron---> NVPTTVFTPLEYGACGHSEEKAIELYGQDNLEVYHS
          |||||||/ |///||||/ <   465bp    > ||||||||||||| || |||||/|/||//|/|||||
  Target  KLLARRLFGGSTVKCDYI                NVPTTVFTPLEYGCCGLSEEKAVEMYGEENIEVYHS
          atcgccctggtagatgta                agcaagtaccgtgttgctggagggatgggaaggtca
          attcggttggcctagaa                tatcccttcctaaggggtcaaactatagaaatataag
          aggccactagcaggtcc                attcctgtatggtactatcaggtgggtaggccggctc


  Query    <---Intron---> LFWPLEFTVPNRDNNKCYSKIICNKLDNDRVI <---Intron---> GFHYLG
           <   154bp    > |||||||||| |||||||/|//|||||//||/ <    81bp    > ||||||
  Target                  LFWPLEFTVPGRDNNKCYAKVVCNKLDSERVV                GFHYLG
                          cttccgtagcgagaaattgaggtaacgagcgg                gtcttg
                          ttgctatctcggaaaagacattgaatagagtt                gtaatg
                          ctggggctctagcccatctgtgtcagctgagt                gcccgt


  Query   PNAGEVTQGYGAAMKCGLTKEQLDNTIGIHPTCAEIFTT <---Intron---> MEVTKSSGGDITQAG
          |/|||||||| ||||||/|||||| |||||||||||||| <   192bp    > ||/|| || ||||||
  Target  PSAGEVTQGYAAAMKCGMTKEQLDITIGIHPTCAEIFTT                MEITKRSGADITQAG
          caggggacgtgggaatgaaagccgaaagaccatggataa                agaaaatgggaacgg
          cgcgatcagaccctaggtcaaatatctgtaccgcattcc                tatcagcgcatcacg
          ccatgccgctaacggccgtgaaaccgttccactagcctc                ggaagaaatcctatc


  Query   CUG
          |||
  Target  CUG
          ttg
          ggg
          cat
           *

SECIS prediction

Predicted by: Infernal (score 38.38)
Covels score: 36.31
Free Energy of structure: -20.1
Target name: JARO01000300.1:subseq_1,97159_
Positions on target: 48179-48256 Strand: +
Distance between candidate CDS and SECIS: 298
Distance between Sec-UGA and SECIS: 301
SECIS grade: A

SEQ CUUUCAUCACGCUGUAUGAUGCCUUGGCCCUUAACCCAGGCAUUGCGGGGGGCCAAGGCUGAUGUCCUCUGAGUGACC
SS ..(({[(((.......{[[{((((((((((((...............))))))))))))}]]}......)))]}))..

Output page