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Sequence 204 Gene Prediction 204j Evidence

     

    Summary

    F-model is better than G for this gene. Based on the evidence below, I would like to name this gene (located in 176135  - 182686)  in maize 'Fiber protein Fb2/ Di 19 domain containing protein'.

    This result has been further confirmed through Maize EST/cDNA database in NCBI.

     

    FGENESH predicted protein

    >FGENESH:   5   5 exon (s) 176135  - 182686   238 aa, chain -
    MDMEVYERLTAETSHYRGTRFDALIGLDEVEPSDEEEDEEEEERAAGAGAGDELLCPFCS
    EELDAVGLWCHMDDEHRAEVNAGVCPICTDKVDMNLIVHISSQHRGFLKIKLSYLTPEIH
    VQDKWRNQQGSSGVRYSTLALLKKDLHERISGSSRAAPVSTVPDPLLSSFVGSFYEVDLP
    KDAKKESLVETEVRSDNIEQRAAESFDEPLLPEVKEEKTRRSQFVQGLVLSLMFDDIL 

     

    Blast results

    Matched to Sorghum, Rice and Populus with e-value range from e-30 to e-105.

    All these matched genes contain a domain called: Drought induced 19 protein (Di19);/db_xref="CDD:147657".  The name of this domain came from this 1995 paper and by that time, researchers only know this domain increased its expression under drought stress. But the function of this domain is unclear.

    Interestingly, beside this domain, most of the genes it matched annotated as a Fiber protein Fb2. I haven’t found the original paper for the function of this protein, however, some clews show this protein may be fist found from some cotton cultivar research.

    Based on the two clews above, I assume that this domain/gene may be coding for some fiber protein in plants, and the expression of this kind of fiber protein increased under drought to deal with stress.


    F-model Blast result

    204j_F_blastp_NCBI.JPG

     

    Conserved Domain

     

    204j_domain search results_di19.JPG

     

    Expression confirmation

    Genome DNA unmasked blast maize EST
    Using sequence 204_ 176135  - 182686 maize EST in NCBI using high similarity
    176135  - 182686
    More than 50 hits e-value < e-90
    The five exons matched very well to the EST, good prediction.

    204j_F_prediction exon distribution.JPG
    204j_Expression confirmation_Blast Maize EST.JPG

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