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Sequence analysis of the second 50,000 bases of smo5 (2259000-2309000)

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    By Nimnara  Yookongkaew

    Gene prediction based on FGENSH (monocot), GENEMARK (rice) and GENSCAN (maize)

    Gene exon compare.jpg

    The alphabet genes are implied as pseudigenes or fragments which could not be predicted based on tblastn.

    tblastn results

    tblastn shot1.jpg

    tblastn shot2 (1).jpg

    tblastn shot3 (1).jpg

    Amino acids comparison

    amino acid compare.jpg

    Amino acid sequences in each gene obtained from tree programs were aligned to determine the comserved region.

    Then, the conserved domains were blasted by blastp (NCBI) together with InterProScan analysis (EMBL) to confirm

    the function domains of predicted peptides.

     

    Gene
    Predicted domain from InterProScan
    Comment
    Gene 15 alignment, blastp
    Calmodulin binding protein
    Same result as tblasn
    Gene 16 alignment, blastp
    Calmodulin binding protein
    Same result as tblasn
    Gene 17 alignment, blastp (no hit)
    Conserved sequence from protein alignment has no hit here
    tblastn hits with calmodulin binding protein
    Gene 18 alignment, blastp
    Glyoxal oxidase, Galactose oxidase
    Same result as tblasn
    Gene 19 alignment, blastp
    Match with ribosomal protein Rsm22 of bacteria??
    tblastn shows some interesting results as copper ion binding mRNA  as well as the result of blastp
    Gene 20 alignment, blastp
    NADH dehydrogenase
    Same result as tblasn, prediction based on GENEMARK only
    Gene 21 alignment, blastp
    Pentatricopeptide repeat domain
    Same result as tblasn
    Gene 22 alignment, blastp
    Hit with SET domian, a domain that appears     generally as one part of a larger multidomain protein
    tblastn hits with Trithorax- related protein (ATXR) but InterProScan and blastp show the same result
    Gene 23 alignment, blastp
    Zinc finger, WD40 repeat protein
    Same result as tblasn
    Gene 24 alignment, blastp
    Serine/threonine protein kinase
    Same result as tblasn

      Conclusion

           Based on the prediction of 3 programs, FGENSH and GENEMARK showed similar results while GENSCAN misseed some genes such as gene 16 and gene 19. Moreover, GENSCAN predicted the psuedogene I and M at the regions that showed no hit from the other programs. Interestingly, GENEMARK predicted two genes in the same regions (at 74341-76625) that contained the significant domains as shown in blastp and InterProScan so the two genes are predicted as gene 20 and 21. On the region around 74341-76625, FGENSH and GENESCAN predicted just one gene (gene 21).


























































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