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Gene 5

    Table of contents
    1. 1. Gene Model Prediction
    2. 2. Evidence
      1. 2.1. cDNA
      2. 2.2. EST
      3. 2.3. Proteins
    3. 3. Conclusion

     

    Gene Model Prediction

    Gene predicted consists of 2 exons on the reverse strand:

    Witin 150kb region coordinates are:

    FGeneSh
    Exon Start Stop
    1 142412 142456
    2 142968 143528

     

    Witin predicted gene region 141659 - 143980 (2321 bp) coordinates are:

     

    FGeneSh
    Exon Start Stop
    1 753 797
    2 1309 1869

     

    >FGENESH:[mRNA] 5 2 exon (s) 142412 - 143528 606 bp, chain -
    ATGCGCCAAGACGAGCAGCAGCCAGTGTACTCGTCGTCGTCGCTGTCCTCCACGCGCTCT
    CTCTCCATCGACAGCGGGGGCTCCTCCTCCACGTTCTTCCCGCTCGACTACGACGCTGTC
    GCCGCCTTGCCCGCCGCCACCTTCTCGCCGGCGCCCCTGCAGCTTCAGCAGGACCCGTTC
    GCCGGGGACGAAGAGGCCATGATGCTGGCCATGCTGGCCGTCATCTCCTCCGCCGCGTCC
    ACGTCGCCCTCCTCCTCCGAGTCCTCGTCACCGCTGCACAGAGCCGCCGCCGCCGTGCAG
    CCGCGCCTACACCCTCACGGCGGGGACGACAGCGCCAGCCACGTGACTGTCAGGAGTACC
    AGCCTCGCCGTGGCGCCGGAGAGGACCACCAGCGCCGCCGACGCAGCAGGGCAGCAGGAC
    GACGCCTGCAAGGCGGCTGCGGCGGCGGCGGGGAGCAACAACAGCAGCCAGGTGTACCAC
    ATGTTGTCCGAGAGGAAGAGGCGGGAGAAGCTCAACGGCAGCTTCCACACGCTCAGGTCG
    CTCCTCCCGCCGTGTCCCAAGATCCGTTGCAACAACGTGACCTGCACTATTATAGACATG
    GTCTAA
     
    >FGENESH: 5 2 exon (s) 142412 - 143528 201 aa, chain -
    MRQDEQQPVYSSSSLSSTRSLSIDSGGSSSTFFPLDYDAVAALPAATFSPAPLQLQQDPF
    AGDEEAMMLAMLAVISSAASTSPSSSESSSPLHRAAAAVQPRLHPHGGDDSASHVTVRST
    SLAVAPERTTSAADAAGQQDDACKAAAAAAGSNNSSQVYHMLSERKRREKLNGSFHTLRS
    LLPPCPKIRCNNVTCTIIDMV

    Evidence

    cDNA

    According to MaizeGDB there are no ESTs or cDNAs in this region

    maize gdb view.jpg

     

    NCBI Blastn against nucleotide db:

    Full results here

    Summary:

    gene 5 blastn to nucleotide db.png

    Top hit is alignment region apanning 224 - 751 (left side) of query to a retrotransposon/helitron. Other hits are alignments to various maize sequences and weak (~90% matching or lower) alignments segments of various proteins. Would expect the multiple, non consistent matches to be consistent with the insertion of a helitron at this location.

     

    Alignment of query to HLH structure.png

    The alignment of the right side of the query (1310 - 1958) corresponds to exon 2 of the predicted gene model. All three hits to this region weakly match ~80%, one of the hits is a HLH binding domain (alignment above).

    EST

    PDF of full results here

    There are ESTs that map to the query, but at fairly low confidence. The top hits align to the 5' end (right) end of the sequence and support the gene model. However the match is only 80%, and after that confidence of the hits drops off. Cannot say with certainty that the region is actually expressed, especially considering that no ESTs or cDNA are located in the region in MaizGDB.

    est alignment.png

     

    Proteins

    Full blastp results here, query is protein sequence predicted by FGeneSH

    blastp results.png

     

    Conclusion

    The predicted region resembles a HLH binding region, which according to NCBI is common in DNA-binding proteins such as transcription factors. However, the predicted gene model seems to be located within a helitron since the part of the predicted model just downstream of the HLH region matches strongly (E.value=0) to a transposon/helitron region. The other cDNA hits in the region are from various other proteins with no common trend observed.

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