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Gene 1

    Gene 1 Model

    4 exons on the reverse strand, so exon 4 is most 3' and exon 1 is most 5'

    gene model table.jpg

    Coordinates of start and end relative to start of gene region in parentheses.

     

    Predicted coding sequence:

    Gene 1 model coding sequence.jpg

    Evidence:

    Predictions from softwares

        FGeneSH Prediction GeneMark Prediction
    Exon Strand Start End Start End
    1 - 46157 46173 --- ---
    2 - 45862 45979 --- ---
    3 - 45649 45656 --- ---
    4 - 45431 45593 45431 45550
    5 - 45230 45349 45230 45349

     

    *Cells highlighted the same color indicate similar predictions made by the two softwares.

    Gene region (transcriptional start site (TSS)) to poly-A predicted by FGeneSH: 47228 to 44007 (reverse strand)

    FGeneSH coding and protein sequence prediction:

    >FGENESH:[mRNA] 1 5 exon (s) 45230 - 46173 426 bp, chain -
    ATGACAAGATTTATCAGGTCAAACAATGGACTTCAGAACACAGAACAACAAAAGATATCC
    AAGTATATCAACACACATGTTACAGAGGCTTTCCCTATGAGAAAAGCAGGAAAGTTTGGT
    AACGAAAATTGCAAGAACTTTAGGGGTCATGGCGACTCTGCTAAGTTGGACACTTTTGTT
    CCATCCATGGAGGCTGCAAAACCAGGTTTCAAGGAAGTTGAGAAATGGAGTGAAAATGCT
    TTGTGGAGTGTATCTGAGCTTCATGTTGGCGATGAGAAGCAGACTGGTTCTAACAAATCT
    GATATGGAAAGAGTACTAAAAGGGTTTGGAGCTTGTGATGCTTTTGTGGCTTCTAGGCTC
    AACGCCCCTAATGGACAAGTTGGTGGTATTACGTTTAAGTCTTCAGACATTGCCCTTCTA
    ATATGA
     
    >FGENESH: 1 5 exon (s) 45230 - 46173 141 aa, chain -
    MTRFIRSNNGLQNTEQQKISKYINTHVTEAFPMRKAGKFGNENCKNFRGHGDSAKLDTFV
    PSMEAAKPGFKEVEKWSENALWSVSELHVGDEKQTGSNKSDMERVLKGFGACDAFVASRL
    NAPNGQVGGITFKSSDIALLI

    Expression Evidence

    NCBI blastn to est database

    Click here for PDF of results

    cdna est table.jpgResults provided support for four putative exons.

    Alignments to predictions:

    PDF of full blastn to NCBI est db here

    PDF of full blastn to NCBI nucleotide db here

     Perfect Alignments.jpg

    some alignment 1.jpg

    some alignment 2.jpg

     

    No alignment.jpg

    Maize GDB ESTs

    maize gdb est.png.

     

          Coor. Withhin Predicted Region
    EST Start End Start End
    37375054 138845030 138845929 1022 1921
    211096117 138845039 138845774 1031 1766
    211384078 138845217 138846101 1209 2093
    166550353 138845074 138845176 1066 1168
    166451346 138845159 138845253 1151 1245

    Protein Predictions

    PDF of full results here

    gene 1 model blastx results.jpg

     

    Blastp of FGeneSh predicted protein sequence:

    blastp of FGeneSH predicted protein.png

    Overall Conclusion

    Blastx results show a few matches to hypotethical proteins in rice, sorghum, and other plants. The matches are overall fairly weak, the strongest match has a E.value of 10^-30. No matches to common domains or motifs were found.

    Blastx of the whole ~3kb region predicted by FGeneSH produces similar results in all ORFs so the lack of protein support is likely not due to a grossly incorrect model. Blastp of the FGeneSh predicted protein sequence (FGeneSH model not vastly different than our proposed model) did not return any results.

    Given the strong support of the model and overall expression of this region and lack of protein support it is possible that the region is a maybe coding for an ncRNA of some sort. The possibility also exists that there has not been work to characterize the encoded protein transcribed from this region.

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     blastp of FGeneSH predicted protein.png
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     gene 1 model blastx results.jpg
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    Gene 1 model coding sequence.jpg
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     gene model table.jpg
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    NCBI Blast_Gene 1 whole sequence est blast.pdf
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     NCBI Blast_Gene 1 whole sequence nt blast.pdf
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    NCBI Gene 1 blast x of CDS.pdf
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     No alignment.jpg
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     Perfect Alignments.jpg
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     some alignment 1.jpg
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