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Gene 2

    Gene 2 was predicted by all three gene prediction programs - AUGUSTUS, FGENESH, and GeneMark.

    Gene id Exon id Type Start End Sense
    2 8 Terminal 32122 32172 -
      7 Internal 32268 32483

    -

      6 Internal 32557 32853 -
      5 Internal 32930 33241 -
      4 Internal 33370 33489 -
      3 Internal 33533 33676 -
      2 Internal 33744 33851 -
      1 Initial 34038 34481 -

     

    The predicted nucleotide sequence is:

    >gene2

    ATGGAGTTGATGGGAACATGCGCGGCCCCCGGGGGAAGGATGTCTTCGCCCGAGCTCCGG
    GAGTCTTCGGCGCGGATGCTGGAGGTTACCGGGGGTCGATGGCCCAAGGACGTTCCTATC
    CCCCGCGCGGCCGGCGAAGACTTTTTTACGTCTCGCATGGCTCGTGACTTGAGAGTGCTT
    CCTTACGGACGAAATATTGCTGCTGTTGTGTCGACAGTGATGAACAAGGATCGCCAGGAA
    GCTGCGCAGAAGCGTCAGGCGGTCATCAGGCTCCCCAAAGCTAGGCCGAAGAGGGCGCGG
    GGGACTGCGAAGGCTACCGTCCCCGGCGGTAGCCAGCCGACGATGGCGGCGAAGCCGGTC
    GCCCCTGGGTCCAGCAAGGTGCTGGAGAGCGTGAAGGCGGCCGGCGCCGGCGGAACCAAG
    TCTGCCCCGGACGGAGCTGCGAAGGTCCGGGAATTGCCTTAGCCGAGGAAGCACGTTGCC
    GACTTCGGCACAGATATTAGCGTGGACGACTATCTCGTTGGTAAGCATTTTTTTGACTGG
    TGATACGTTGCAGGATCGGGCGAGGGGCAACATGTTGTTGTTCCGCCTGCGGTGGCGACC
    ACGACGTCTGTCGCGGTGGTTGGGGTGAAGGGTAGCGCTTTCAGCGCTGGCGGCGAGATT
    TCGGCGGTCACTGCCGTCAAGGACGAAGCGGGCACTGTGTCCCGCCGGCTGAGGGAGGTG
    TCGCAGCGGCTGAGTCAAGTAAGTTGAGCTGGACTTCGGTGTTTACCGCTTTCATGGGGA
    TTGTGGTCTCATGTGTGTCTGTTAGGCGGCCGACTTCGCCGACCGCGTGGCGTCGGGGGC
    CCTTACTGCAGATGTGTCTGCCGAAGTCGAGAGACTTCGGGCGCAGCACGCTGACGCCGT
    CCGGGAAAAGTCGGCTGCGGATAGCAAGTGCCGCAAGCTGGCGGAGAAGGTGGCCCGCCC
    TGGAGGGCGAGAGGACGGACCTCCGGCGCCAGATGGTGGAGGAGAGGAGGGAGGCCAACC
    AGGCCATCGCCAAGGCGCAGGCGGCAAAGGCGGAGGCCAAATTGGCGCGGGTGGAGGGGA
    GTCTCGCCAGCCAGCGCGCCGAGGAATGGGAGGTGCAGTTCAACGCTCTGCAGGCCCGCA
    TGGAGAGGGCCGAGGCCTCTACGCGCTCGGAAGTTGAGCGGACGCGCAAAAGCTCGTGGA
    CTCATACCGCGAGCTGGGTGCGTGGACTGCTGACTTCGAGGTGCCCGACCGAGAGGCGGG
    CCTTCGCTTCCTCGAGTGGCTGCAAGAGGAATTGTTGGCGCTCCCGACCATCGTGGAGGG
    ATTCATGTCCTTTGCCTCCCTCGTTACCTGCGAAGGGGCTATGAACGCGCTGTCCCGCGA
    GGCGTGCAGTCACTATGAGGTCTTCGACCGATCCGATGAAGACTTTGGGCGCGAGATTTT
    TAAGGTCGAAGACTCTGTGGTGAAGGACTCTGCGGGGGCCCTCTTCGACTGGATGTGGGG
    CCCCTACGGTCGGGAGGTGGTTAGGGAGCGGTCTGACCGGGCGAGGGATCAGGTAAAGTT
    TGTCTTTTGTTTAGTGTCGTTGAATGTGGGTATACGTGGGCTTACTGAATCGGTGTGCTG
    TGTTGTAGATGGTGCGTGCCGAGGATGTGGAGGACTTCGGACCCCTGAATAGCGTGCAGC
    CCGAAGCGGAGGCCAATTCAGTGGTGGTCGAGGCTGAGGTCGGCCCGGCAGCGCCCCAGG
    AAACCAGTGAAGGCTCCCTCGCTGCCCCTATGTCTACTATGTCCGGTGGAGGCTCGTTGC
    CAGCCACTGTGCCGATGGTGGAGGATCCCCCGAAGGCGGCAACGGAGCTGGCAGCGGAGG
    CTCCCCCGAAGGCGGCGACGGAGCCGGCAGCGGAGGATCCCGTGGCGGCGGCTGGGTCTT
    CGCAGGTGGCTTAGTGGGTGTGGGGTAGTTAGAGAATTTTGTCTATGTTACTGAACCTTG
    GTTGCTGCACAGGTTCAGGATTTTGGGCCTGCGCACGCAACCGCTACTGCTAATTTTGTG
    GCGGCTTCGACCGTGGTCGCTGGAAATGAATCGGATGAGTCTAAGTTTTCTGATTTTGAT
    GACTCTGGGAGTTCGGTTGAGTGGACGGAAGAGTCTTCGGATGAGGACTTGGATTACTTT
    GCGGCCTTGGATGTGGCTGCTGCGGAGGCTTCTCCGCGTGTTACGGATGCTGAAGTTTTG
    CCTAGTCCGAGTGCTGGGCGTAGGTGGCGAAGGGAGGTGGCGAAGCGTAGAGTGAGTGAA
    GTGGATGGCGGTCGACTTCGTGTGGGCAGGGCTGGCAAGCGGGAATTGTTGTCCTCGTCG
    GTTGGGGCGAGTGTAGGTGA

     

    The predicted amino acid sequence is:

    >gene2

    MELMGTCAAPGGRMSSPELRESSARMLEVTGGRWPKDVPIPRAAGEDFFTSRMARDLRVL
    PYGRNIAAVVSTVMNKDRQEAAQKRQAVIRLPKARPKRARGTAKATVPGGSQPTMAAKPV
    APGSSKVLESVKAAGAGGTKSAPDGAAKGSAFSAGGEISAVTAVKDEAGTVSRRLREVSQ
    RLSQAADFADRVASGALTADVSAEVERLRAQHADAVREKSAADSKCRKLAEKMVEERREA
    NQAIAKAQAAKAEAKLARVEGSLASQRAEEWEVPDREAGLRFLEWLQEELLALPTIVEGF
    MSFASLVTCEGAMNALSREACSHYEVFDRSDEDFGREIFKVEDSVVKDSAGALFDWMWGP
    YGREVVRERSDRARDQMVRAEDVEDFGPLNSVQPEAEANSVVVEAEVGPAAPQETSEGSL
    AAPMSTMSGGGSLPATVPMVEDPPKAATELAAEAPPKAATEPAAEDPVAAAGSSQDFGPA
    HATATANFVAASTVVAGNESDESKFSDFDDSGSSVEWTEESSDEDLDYFAALDVAAAEAS
    PRVTDAEGWQAGIVVLVGWGECR


    When doing a blastp search, the top hit was uncharacterized protein LOC100382558 [Zea mays] with a 52% identity and an E-value of 2E-88.

    EST evidence

    Doing a Blastn search against the EST database, we get the following result.

    We find good EST evidence for two exons - exon 2 and exon 4. Exon 4 was the most prominent exon match. The top hit for EST was 25700533 CERES-CB5 Zea mays cDNA clone 1158101 3', mRNA sequence with a 91% match and an E-value of 2E-104. We think this is a pseudogene or an incomplete gene as well whose evidence is present at the mRNA level.

    Protein function prediction

    Pfam gave us a 0.45 E-value hit of Seryl-tRNA synthetase N-terminal domain match. Blast2GO gave the function as Zinc ion binding, and the cellular component as intracellular.

    kpadmana 10 December 2012

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