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Gene 3

    Gene 3 was also predicted by all three gene prediction algorithms. It is one of the most promising genes in the region of sequence we got. The gene and exon coordinates of the gene are given in the following table.

    Gene id Exon id Start  End Sense
             
    1 17 64642 64878 -
      16 64965 65061 -
      15 65149 65243 -
      14 65426 65530 -
      13 65656 65817 -
      12 65913 66009 -
      11 66092 66354 -
      10 66439 66563 -
      9 68051 68082 -
      8 68377 68468 -
      7 68549 68617 -
      6 68696 68854 -
      5 68945 69001 -
      4 69083 69145 -
      3 69231 69278 -
      2 70573 70698 -
      1 71032 71049 -

     

    The predicted coding sequence is

    >gene3

    atgggccacaaaacaaagctaattgatggagatgggatcttcaacgtctccggattggagaacttcatgaaggatgtcagattgggtgaatgcgggct
    gtcctatgctgttgtatcaataatgggcccgcaaagtagtggtatgacacccctagaaaatcttgagccaattctaagggaagacattcagaagatat
    gggatgctgttccgaaaccccatgcccataaagaaactccaattagtgaatttttcgatgttcaagttgtcgcactgtcgagttatgaagaaaaagaa
    gagttattcaaacagcaggtttctgatttaagagataggtttcagcattcaattgcccctggtggacttgctggggatcgtcgtggtgttgtcccagc
    ttcaggtttctcatttagttcccagcaattttggaaagtcatcaaggagaacaaagatcttgatttgcctgctcataaagttatggtggctactgtac
    gttgtgaggaaattggtaatgagaaagttaccagctttatagctgatgaggaatggcaacaatttgaggaggctgtccaacatgactttgttactggg
    tttgggaagaagctcagcagccttctggatagatgtttatcagagtatgacatggaggctatttattttgatgaagatgctgctattcaacaagtgaa
    ttgggacacctcaaaagtgagggataagcttagacgtgacattgaggctcatgtagcttcagttcgggctgctaaattgtctgaactttgtgcgaaat
    atgaggcacaacttaccaaagctctggtggaaccagttgaatctcttctagattcagccagtgaagacacgtggccagctattagaaagcttcttcaa
    cgcgagacaaaaactgctgttttaggtcttgaatctgctgtgtcagcttttgaactcgatgaagcaactgagaaagaactgcttgcgaagctggagaa
    gcatggaaggagtgttgttgagtcaaaggcaaaagaagaagctggaagggttttgattcgcatgaaggacaggttctcaacattgttcagccgagatg
    ctgactctatgcccagggtgtggacaggaaaggaggacataaaagctataactaaaaccgctcgctcagcttctgtgaagttgctttctacaatggct
    gcaattcggttggaggaggatggtgataacattgagaacactctttcccttgctcttgttgacacttcaagacatgggactacagataggagtatcca
    attgtccgatccactagcctccagctcatgggaaagggttgctgaggagaagactttaattacccctgtgcagtgcaaaaatttgtggaggcaattca
    aagctgaaactgaatatacagtcactcaagccatagctgctcaggaagcaaataagaggaacaacaactggctcccacctccatgggcacttgctgca
    atggctatccttggattcaacgagtttatgacattactgaggaatccgctttacctgtttgccatatttgtgatttatcttgttggaaaagccctttg
    ggtgcaatcagaaattggcagggaattccaacatggatttcttcctgccatcctttcactgtcgacgaaatttgttcccactgtaatgaacatcctga
    agagattagctgacgcgggtcaagaacctgcagcagcccccgagaggcaaagagagatggagctccaaccaaaatccaccaggaacggttccttatac
    agcaatgtgacatcggcagggtcatctagcgtaaccacttcggagattggacctgaatattcaagcccggttgtgcaatga
     

    The predicted amino acid sequence is:

    >gene3

    MGHKTKLIDGDGIFNVSGLENFMKDVRLGECGLSYAVVSIMGPQSSGMTPLENLEPILREDIQKIWDAVPKPHAHKETPISEFFDVQVVALSSYEEKE
    ELFKQQVSDLRDRFQHSIAPGGLAGDRRGVVPASGFSFSSQQFWKVIKENKDLDLPAHKVMVATVRCEEIGNEKVTSFIADEEWQQFEEAVQHDFVTG
    FGKKLSSLLDRCLSEYDMEAIYFDEDAAIQQVNWDTSKVRDKLRRDIEAHVASVRAAKLSELCAKYEAQLTKALVEPVESLLDSASEDTWPAIRKLLQ
    RETKTAVLGLESAVSAFELDEATEKELLAKLEKHGRSVVESKAKEEAGRVLIRMKDRFSTLFSRDADSMPRVWTGKEDIKAITKTARSASVKLLSTMA
    AIRLEEDGDNIENTLSLALVDTSRHGTTDRSIQLSDPLASSSWERVAEEKTLITPVQCKNLWRQFKAETEYTVTQAIAAQEANKRNNNWLPPPWALAA
    MAILGFNEFMTLLRNPLYLFAIFVIYLVGKALWVQSEIGREFQHGFLPAILSLSTKFVPTVMNILKRLADAGQEPAAAPERQREMELQPKSTRNGSLY
    SNVTSAGSSSVTTSEIGPEYSSPVVQ

    When a BLASTP is done, the top hit that we got was a 86% match to SEY1 protein with an evalue of 0.0 and a coverage of 99%. We think there might be a slight variation in the gene model since there is only a 865 match even though there is good coverage.

    EST evidence:

    We found very good evidence for three exons, with 100% match to a Zea mays cDNA mRNA sequence. In some cases, there are three exons instead of two exons. This could be a splice junction error or an error with the gene model.

    Protein function prediction:

    When we tried Pfam prediction, we found that the protein contained the RHD3 domain, which we also found during the blast search. The protein SEY1 has a function of generating and maintaining the structure of the tubular endoplasmic reticulum network, and has GTPase activity. The RHD3 domain functions to regulate cell enlargement and membrane trafficking.

    From Blast2GO results, we got the cellular component as membrane protein, and ER, process as root epidermal cell differentiation and cell-tip growth, and the function as hydrolase activity and GTP binding.

    kpadmana 10 December 2012

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