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Seq 206-4 detailed analysis

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    1. Seq from F:

    >FGENESH:   2  12 exon (s)  51764  -  57416   735 aa, chain +
    MATSNSRATALSLISSPSFSLDYFPAAGAIAQLALSRGASANATVGTISMPNPDARDPAA
    EGQDLPHQLAVTAHLFTAAAIHGVLRLESWTVHPPPQPLIFLTPPPLFTPLCQQNRARAG
    ERTQQTAVKHGRRWIGGRNGVTNNCGTPGVRCGTGGFLGEDRGTVGAWYFRFARLKPVFS
    PHLLTIRERISVGNDGGPVPVRLLSDLFDEAKKAIDEAIESENGSLTHFEVFTALSFLLF
    SQQNVDIAIIECWRNDVEATEKVEDMLKILDWMTNVTEGVGGGLYALVAVDGSVALLHGV
    ELMAEEDGLRILVGSPNLLHKVLKWDAHLVGLLHRQCHGDVGLDVGSGIVVGDHHRLLLV
    VGGMSSVVDVAGLGGARDATNVIRSTELAASVITTVGREHLVALGGSLQSIAIAKSGIIK
    QGRPVVIGGPFSEDIEQIIRDRAFLTQSPVISACGHGIKSFTKCIDWDNGKPYQRCYISI
    KISRDVPLSIEMHDINLQLLGDHQRQNAVTAACAALCLCSQGWDISDASIQAGLEETQLP
    GRSQFLTAEEASALGFDSASTVLIDGAHTEESAKALSGVIKTVRPEGPLALVVGMASDKE
    HLAFAEQLLSGQTPDVVLLTEASVAGGTSRAMPASSLKEVWIAAARDRGIEYVDIGGVSG
    AETPEHISDLLDCSPSSNSGRKPMVIGCQDVAPFSSNLIVAASQLLESRGTAPGLICVTG
    SLHLVGAVLQQMGRH

    Get the following result from BLAST:

    seq 206-4 from F-1.bmp

    seq 206-4 from F-2.bmp

    It seems that it is the GLA1 gene in Zea mays whose e-value is 0. In addition, in the sequence, there are two domains, PLN02913 and  Mur_ligase_M.

    Besides, the sequence also have a good e-value (0) match to the hypothetical protein SORBIDRAFT_08g017730 [Sorghum bicolor]. The Sorghum bicolor has three domains on the hypothetical protein SORBIDRAFT_08g017730, PLN02913,  Mur_ligase_M and Mur_ligase_C.

    However, we found that there are only one domain at this part of sequence, PLN02913 (dihydrofolate synthetase), which can match to the GLA1 gene in zea mays and hypothetical protein SORBIDRAFT_08g017730 [Sorghum bicolor]. See the picture of the domain below.

    Domain of PLN02913.bmp

     

    This sequence also matches to the GLA1 (GLOBULAR ARREST1); dihydrofolate synthase [Arabidopsis thaliana]. So we guess it is a gene containing the PLN02913 domain or dihydrofolate synthase.

     

    Compare the masked sequence from position 50764 to 58416 with the Arabidopsis sequence,

    maize compare with arabidopsis.bmp

     

    2. Seq 206-4 from G

    Also get the similar result, find domain PLN02913 (dihydrofolate synthetase).

    3. Compare with maize EST

    Input orginal sequence from 50764 to  58416. There are 183 blast hit on the query sequence.

    206-4 compare with maize EST.bmp

    4. Further analysis by using Interproscan

    206-4 further analysis.bmp

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