Was this page helpful?

Gene 4.2

    Gene Model

    Exons 2, 3, 4, and 5 from FGeneSH combined make the best gene model for the region. A four exon model agrees with the annotated gene model in MaizeGDB (GRMZM2G165428).

    maize gdb 4 exon gene model.jpg

    When exon 1 from either the GeneMark predicted model or the cDNA supported model is added the reading frame of the protein is shifted such that the protein kinase-like (Pkc-like) superfamily region is truncated. Below are all the models along with their resulting coding sequence.

    FGeneSH

    FGeneSH Model
    Exon Start End  
    1 109800 110001 201
    2 110573 110833 260
    3 110920 111810 890
    4 112287 112756 469

     

    This model is supported by the FGeneSH prediction and exons 2, 3, and 4 (same as exons 3, 4, and 5 of GeneMark model and cDNA-supported model) are supported by multiple cDNA alignments (see expression evidence section); exon 1 has partial cDNA support and exons 2, 3, and 4 have cDNA support for the exon as a whole and the coordinates of their boundaries. There are also >10 EST sequences in support of the overall region.

    Gene 4.2 FGeneSH model.jpg

    GeneMark

    GeneMark Prediction
    Exon Start End Size
    1 109263 109393 130
    2 109772 110001 229
    3 110573 110833 260
    4 110920 111810 890
    5 112287 112756 469

     

    This model is supported by the GeneMark prediction and cDNA support; exon 2 has partial cDNA support and exons 3, 4, and 5 have cDNA support for the exon as a whole and the coordinates of their boundaries. There are also >10 EST sequences in support of the overall region.

    Gene 4.2 cDNA GeneMark model.jpg

    cDNA Supported Model

    cDNA supported model
    Exon Start End Size
    1 109546 110001 455
    2 110573 110833 260
    3 110920 111810 890
    4 112287 112756 469

     

    The start coordinate for exon 1 of this model was determined by the alignment of the query sequence to a hypothetical sorghum protein, where base 1 of the sorghum protein matched base 283 (109546 in the 150kb region) of the query. See the alignment below:

    Gene 4.2 hypothetical sorghum protein alignment for cDNA model.jpg

    The rest of the exons were supported by cDNA evidence of the same hypothetical sorghum protein along with 3 other high scoring (E.value >= 8e^-176) cDNA matches (see expression section). >10 EST sequences also covered the area. The cDNA-supported model results in the below coding sequence.

     

     

    Gene 4.2 cDNA supported model.jpg

    Predictions

        FGeneSH Prediction GeneMark Prediction
    Exon Strand Start End Start End
    1 + - - 109263 109393
    2 + 109800 110001 109772 110001
    3 + 110573 110833 110573 110833
    4 + 110920 111810 110920 111810
    5 + 112287 112756 112287 112756

    Evidence

    EST evidence from MaizeGDB

    -No cDNA hits in this database

    est cDNA from MaizeGDB.jpg

    EST from NCBI est db

    PDF of full results here 

    Highlight of alignments below:

    Gene 4.2 blastn est db alignments.jpg

    Heavy (>10) EST alignments to areas associated with exon 1/2, 3, 4, 5. Below is GeneMark model with coordinates relative to the start of the region (109,263) for comparison to EST alignments:

    GeneMark Prediction  
    Start End Size
    1 130 130
    509 738 229
    1310 1570 260
    1657 2547 890
    3024 3493 469

     

    cDNA from NCBI

    PDF of full results here

    Gene 4.2 whole sequence blastn nr nt cDNA.jpg

    Top 4 hits (E.value >= 8e&-176) provide varying cDNA support for all 3 gene models. See Models section above for specific details.

     

    Protein

    The FGeneSH model produces the most complete alignment to Pkc_like superfamily protein.

    A PDF of the blastx alignment is here

    gene 4 blast x fgenesh alignment.jpg

    The resulting coding sequence of the other two models do align to the PKc_like superfamily region, but their alignments are truncated, likely due to a framshift in the models.

     

    Conclusion

    The FGeneSH model is best supported by the evidence as being the correct model encoding a putative PKc_like superfamily enzyme, speccifically a cysteine-rich receptor-like protein kinase as suggested by the 10+ blastx hits with E.values ranging from 6e^-39 to 5e^-43. See PDF of results in protein section. 

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

    Files 12

    FileSizeDateAttached by 
     est cDNA from MaizeGDB.jpg
    No description
    310.28 kB12:38, 3 Dec 2012tiedeActions
     gene 4 blast x fgenesh alignment.jpg
    No description
    31.04 kB13:09, 3 Dec 2012tiedeActions
     Gene 4.2 blastn est db alignments.jpg
    No description
    71.7 kB12:43, 3 Dec 2012tiedeActions
     Gene 4.2 cDNA GeneMark model.jpg
    No description
    213.4 kB11:16, 3 Dec 2012tiedeActions
     Gene 4.2 cDNA supported model.jpg
    No description
    216.09 kB11:16, 3 Dec 2012tiedeActions
     Gene 4.2 FGeneSH model.jpg
    No description
    196.4 kB11:16, 3 Dec 2012tiedeActions
     Gene 4.2 hypothetical sorghum protein alignment for cDNA model.jpg
    No description
    158.81 kB12:24, 3 Dec 2012tiedeActions
     Gene 4.2 whole sequence blastn nr nt cDNA.jpg
    No description
    195 kB12:50, 3 Dec 2012tiedeActions
     maize gdb 4 exon gene model.jpg
    No description
    12.32 kB11:13, 3 Dec 2012tiedeActions
     NCBI Blast_Gene 4 blastx for FGeneSH model.pdf
    No description
    1647.21 kB13:08, 3 Dec 2012tiedeActions
    NCBI Blast_gene 4 cDNA.pdf
    No description
    470.66 kB12:52, 3 Dec 2012tiedeActions
     NCBI Blast_Gene 4.2 blastn est db.pdf
    No description
    1318.79 kB12:42, 3 Dec 2012tiedeActions
    You must login to post a comment.