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Gene 2

    Gene 2 Model

    cdna est table gene 2.jpg

    Coordinates of start and end relative to start of gene region in parentheses.

    Coding sequence from the model matches the coding sequence of 1-aminocyclopropane-1-carboxylase oxidase 1 (GenBank: ACG35410.1) provided by MaizeGDB, see below.

    sequence of candidate model.png


    Prediction from softwares

        FGeneSH Prediction GeneMark Prediction
    Exon Strand Start End Start End
    1 + 61318 61426 61318 61425
    2 + 61545 61789 61545 51789
    3 + 61911 62499 61911 62499

    Model predicitons exactly same for both softwares.

    Alignment to candidate gene: 1-aminocyclopropane-1-carboxylase oxidase 1

    Accession ID Query Range Relation to Predicted Exons % Match E. Value
    Gene ID: 100283053;  1-aminocyclopropane-1-carboxylase oxidase 1 Gene2:mRNAcds1.3 720 - 1524 3 99 0
    Gene2:mRNAcds1.2 354 - 599 2 100 5e^-124
    Gene2:mRNAcds1.3 35 - 237 1 100 4e^-100


    The models predicted by FGeneSH and GeneMark predicted the middle exon well but missed part of the coding sequence on the 5' end of exon 1 and the 3' end of exon 3. The bases highlighted in red are the bases missing from the models predicted by the software.

    alignment to candidate gene 1.jpgalignment to candidate gene 2.jpg


    Click here for PDF of EST and cDNA evidence from MaizeGDB

    MaizeGDB accession 195627159 (image below), complete coding sequence of 1-aminocyclopropane-1-carboxylate oxidase

    cDNA of candidate gene, accession 195627159 on MaizeGDB
    Exons Start in REF Seq Stop in REF Seq Start in 150kb Stop in 150 kb
    3 138861225 138862714 35 1524


    cDNA from MaizeGDB.png

    Also >10 ESTs that support the gene model.


    The gene models provided by MaizeGDB are not consistent with the expression evidence, the model provided above is more consistent.


    Click here for PDF of complete results from NCBI

    -There are >10 ESTs that confirm this model from NCBI est database


    Model coding sequence blastx to NCBI swissprot database results here

    -blastx results of coding sequence are the same as the blastp results using the coding sequence of 1-aminocyclopropane-1-carboxylate oxidase 1 obtained from NCBI

    blastp results when using candidate gene AA sequence from NCBI as query

    1-aminocyclopropane-1-carboxylate oxidase 1 is a 318 aa protein, sequence given below.

    mtgpmeipvi dlgglnggge ersrtlaelh dackdwgffw venhgvdapl mdevkrfvyg
    hyeehleakf yasalamdle aatrgdtdek psdevdwest yfiqhhpktn vadfpeitpp
    tretldayva qmvslaerla ecmslnlglp gahvaatfap pfvgtkfamy pscprpelvw
    glrahtdagg iilllqddvv ggleflraga hwvpvgptkg grlfvnigdq ievlsagayr
    svlhrvaagd qgrrlsvatf ynpgtdavva papgrddqga gaaaypgpyr fgdyldyyqg
    tkfgdkdarf qavkkllg

    Results of NCBI blastp of above sequence here

    Blastp domains and protein alignment.png

    To summarize, top 10+ hits align to 1-aminocyclopropane-1-carboxylate oxidase 1 protein in many other species; highest E.value 2e^-106. See table below for top 8 hits:

    Organism % Match E.value
    Arabidopsis thaliana 50% 2e^-105
    clove pink 43% 5e^-86
    Indian rice 45% 5e^-85
    Japanese rice 45% 3e^-85
    Kiwifruit 43% 7e^-85
    Arabidopsis thaliana (L.) Heynh 43% 4e^-83
    Apple 42% e^-82
    Tomatoe 42% 4e^-82


    The high scores and multiple alignments to the  1-aminocyclopropane-1-carboxylate oxidase 1 protein across many different species, along with an almost perfect cDNA match to maize suggest that this gene model encodes a homolog to 1-aminocyclopropane-1-carboxylate oxidase 1. According to NCBI this enzyme is responsible for ethylene formation.


    Description of the superfamily domains identified in blastx and blastp, courtesy of NCBI, below:

    2OG-Fe(II) oxygenase superfamily:

    This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC: catalyzing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB.

    DIOX_N superfamily:

    non-haem dioxygenase in morphine synthesis N-terminal

    This is the highly conserved N-terminal region of proteins with 2-oxoglutarate/Fe(II)-dependent dioxygenase activity.

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