Was this page helpful?

Seq 206-16 detailed analysis

    Table of contents
    No headers

    1. At first, use the predicted protein sequence from F:

    >FGENESH:  10   5 exon (s) 396506  - 399962   265 aa, chain -
    MVKEARAPEERLWLGEEHTIAQTLTSLDFWLMFASFLMGVGTGLAVMNNLGQMDVAMGYI
    DVSLFVSMTSIWGFFGRIASGTISEHFIKFFTLSRTALTCASCYSAGTTNKTGPTTQSTY
    KHLSAELGAELGKTQKDLEGTKSALHDLEEKYNEAKSTIKEKEYVIFILLKSGGKGRIPS
    CTCSDDNEWSYKEKIEFTTYFAQEISEGLLFEMEDQIPSLAELIKFGSLLDFQQQCSERY
    RYKDEVQKNAMEILESKIGNWIHFM

    Get the following result using BLAST:

    seq 206-16 from Blastp of F.bmp

    seq 206-16 from blastp of F-2.bmp

    I guess this part belongs to the nodulin family protein which is assumed from the Arabidopsis thaliana.

    So, I did some contrasts. There are two regions in the nodulin family protein, nodulin-like region and Oxalate/Formate Antiporter region. According to the comparison result, we found that the sequence does not match to nodulin-like domain, but matches to Oxalate/Formate Antiporter domain.

    Using the original sequence to compare with Oxalate/Formate Antiporter domain, we got the following result. It still has only 180bp of the sequence that can match, so we do not need to do anymore.

    compare domain with original sequence(206-16).bmp

    At last, I guess it is a gene which contains the Oxalate/Formate Antiporter domain.

     

    2. the Sequence of G

    >Sun Nov 21 16:29:02 EST 2010_4|GeneMark.hmm|gene 4|98_aa
    EARAPEERLWLGEEHTIAQTLTSLDFWLMFASFLMGVGTGLAVMNNLGQMDVAMGYIDVS
    LFVSMTSIWGFFGRIASGTISEHFIKTRAILRPLPTPR

    It is only 98aa, but still get similar answers.

     

    3. use blastn compared with maize EST (expression confirmed)

    compare with maize EST.bmp

    There are distribution of 64 Blast Hits on the Query Sequence. And also have very good e-value.

    4. Further analysis by using Interproscan

    result for 206-16.bmp

    Was this page helpful?
    Tag page (Edit tags)
    • No tags
    You must login to post a comment.