Was this page helpful?

Gene 4

    Table of contents
    1. 1. EST evidence:

     


    Gene 4 was predicted by GeneMark but not predicted by other programs. It has the following co-ordinates.

    gene id exon id start end sense
    4 1 139202 139308 -
      2 139396 139460  
      3 139723 139814  

     

    The nucleotide sequence is:

    >gene4
    ATGGCGGTGGCAGGCGGGCAGGAGCAGGGCCCCGCCATCAGCCAAGCTCATGTCCCATCC
    GGGGGCAGCAAGAGAACCCTCTCTCACGGCGTGAAGACAACGCGCCTGTGCTCCGTTCCA
    CGAACGGCTCACGCACGCGCAACGACCGCCCCGCCAACCACTCGCCCCATCGCATTAACT
    CCGCGGCGGGACAGGCGGCGCCCCTGGCAGGAGAAGCGGGCGACGCTTCGCCTTCGCCAT
    AATGACCGCGTCAAAAAAGGTACGCCGCGTCATTCGATTTCGTATCCTTTTCCTTTTTTC
    CTCTTTCTCTCTCTTGCAACAGGGACCGGGAAAGGGGGATACCCCGAAAAGGATCCTTCC
    CCGTGAAGGAACCAGGCTCCGAGCCTCCCTACTGATCAGAGGTTCGAAGGCTGGCCCCCC
    GGAAGGGTTCGATAGCCGCCTCAGATCGCGTGGGCCCTACACACACTACTGGTCAGAGGT
    TCGAAGGCCGGCCCCCCAGAAGGGTTCCACGGCCGCCTCAGGCTACTCGGGCTCCGCGCC
    CATTACTGATCAGGGGTTCGAAGGCTGGCCCCCGAAGGGTTCACAGCCGCCTCAGACGCC
    GAGCGAGGGATGA

    The predicted amino acid sequence is:

    >gene4

    MAVAGGQEQGPAISQAHVPSGGSKRTLSHGVKTTRLRRPWQEKRATLRLRHNDRVKKGYS
    GSAPITDQGFEGWPPKGSQPPQTPSEG
     

    When doing a blast search against the protein database, the top hit was found to be a putative growth-regulating factor 1 from Zea mays.

    EST evidence:

    The exon seems to have a lot of ESTs that have idenitity > 90%. The top hit is CERES-CB5 Zea mays cDNA clone mRNA sequence with an e-value of 0 and 99% coverage. Since there is no EST with greater than 95% similarity, this is most likely a pseudo gene.

     

    There was no Pfam or Blast2Go result for this gene.

    Was this page helpful?
    Tag page (Edit tags)
    • No tags

    Files 1

    FileSizeDateAttached by 
     Genemark VS EST.xlsx
    Comparasion of Genemark predicted genes with EST database.
    20.01 kB03:20, 29 Nov 2012chen905Actions
    You must login to post a comment.