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Sequence 204 Gene Prediction 204g Evidence

     

    GeneMark Prediction

    >seq204 1600001-2000000 Xiaoqing Yu 09-16-2010_6|GeneMark.hmm|gene 6|99_aa
    MGFEPTTSQANVLVATTTPHEALALASLIDDEKKLSDCQFNLWKQYYLATRVAVFGKLRR
    SHRLDAGDLMVVANAGYYRVVMGTASDNGAVTPSSSSST
     

    Blastp result

    Matched to: Zea mays clone 327862 catalytic/ protein phosphatase type 2C mRNA, complete cds
    GenBank: EU969275.1

    204g_Blastp.jpg

     

    EU969275.1 Sequence


    >gi|195643849|gb|EU969275.1| Zea mays clone 327862 catalytic/ protein phosphatase type 2C mRNA, complete cds
    AAAACCACAATTCACAGGCCCTCTCCGATACTCTTCCTTCCTCGGTCCACCTTTTTTTTCCCGGCCCTCT
    ATCTCCTTAGCTGCCAAGAACACGCTGTTCGATCGTCTCGTGCTAGCGTGGTAGTCTGGAAGCGTCTCTT
    TTTTTTTCTTCTTCCTGTTCGATCCAGTTCTACCCGTCCAATCCAATCCAAGCTCCTCCCTTCACCCCAA
    AGGGACGAGAGATAGAGAGAGAGGTCCTCTATGGCCGGGCCTGCTGTCCACCCTCGTCACGGCAGCCGGC
    CGGCGCTCTGAACTCCCGAGCCGGCTCTCCATCAGCCACGTCGCGCGCCGCCCAGGAGAAGGAGCTCTTT
    AATCTGTGCTAGCAGCGGTCCCAGAGAATGCGGCAGATCTCGTCGCTGCTGCAGGGCCTGGCCCGGTCAC
    TCTCGGTGGGGAGGGACAGGGACAGGGACAGGAAAGGGAACGGCGCAGGCGACGGCAAGACCGCCGTGCC
    GGCGGTGCTGCGGACGTCGGGCACCCTGTGGGGCGACGGCTCGGACACGTTCGCCGCCGTCTGCTCGCGG
    CGCGGCGAGAAGGGCATCAACCAGGACTGCTCCATCGTCTGGGAGGGATTCGGGTGCCAGGAGGGCACCA
    TCTTCTGCGGCATCTTCGACGGCCACGGCCCGTGGGGCCACTACGTGGCCAAGGTGGTGCGCGACTCGCT
    GCCGCCGTCGCTGCTGTGCCACTGGCAGGAGGCGCTCGCGCTCGCGTCGCTCATCGACGACGGCAAGAAA
    AAGCTCGGCGACTGTCAGTTTGATCTCTGGAAGCGGTCCTACGTGGCCGCGTGCGCCGCCGTGGACGACG
    AGCTGCGGCGTAGCCGTCGCTTGGACGCGGTCCAGAGCGGTTGCACCGCGCTGTCCATCGTCAAGCAGGG
    GGACCTCATGGTCGTCGCCAACGTCGGCGACTCCCGAGCCGTGCTGGGCACCACGTACGGCGATGGCACC
    ATCGTGGCCGTCCAGCTCACCGTCGACCTGAAGCCCAATCTGCCACAGGAGAAGGAGCGTATCCGGCGGT
    GCAACGGCCAGGTGTACTGCCTCGCCGATGAGCCCGGGGTGCACCGCGTGTGGCAGCCCAGCCGGGAGTC
    GCCGGGGCTCGCCATGTCACGCGCGTTCGGCGACTACTGCGTCAAGGACTGCGGCGTCATCTCGACGCCG
    GAGGTGACGCAGAGGAGGATCGGCGCCAGTGACCAGTTCGTCATCCTCGCCACCGACGGGGTGTGGGATG
    TGCTCTCCAACGACGAGGCCGTGCAGATCGTGGCAGGGACGCTGGACCGGGCGAAGGCGGCCAAGCGTCT
    AGTGGAGTGCGCCGTTCGCGCGTGGAGGCGCAAGCGGCGCGACATCGCCGTCGACGACTGCTCGGCGATC
    TGCCTCTTCTTCCACCCATCGCCGCCGTCGTAGACACGAAAACCTGTAACGTGCCGAAGTCCACGCCAAG
    GAGGAGGGGGCAACTAAATGCACATCTCAAGACAGACTACGATTATTGTGCCCGTGGCGTTCGTAGAGTG
    CACTGCCGCCGTCCACCGTTCAGAACGTGCAGTTTGTCGCGTGAGAGCGACACTCCACGATTAGGAACTG
    CAGCCGGTGCACGGCCAAACAAAAAGATCTCCGGGTTTCACACGTTGCCAGTCAAGATGTACGAGAACAT
    CAGAGAAAAAGTGTAGGAAAGACGCATTTTGTCCTCAAAAAAAAAAAAAAAAAWAAAAAAAAARAAAAAA
    WMAAAAARGGAAAAAAAAAAAAAAAA

    CDS: 378-1433


    Conserved domain

    catalytic-protein phosphatase type 2C conserved domain.jpg

    150-1000 (55aa to 345aa)
     

    EU969275.1 Blast back to Seq204

     

    EU969275.1 Blastn back against 204 sequence.jpg
    Major Matched region
    719-1021 to 143163-142865
    1041-1239 to 142755-142558

    Our matching is: 719-378=340 to 1239-378=960 that is:
    340-960 matched to majority (73% or 620/850) of 150-1000

    Expression confirmation

    Genome DNA unmasked blast maize EST
    Using sequence 204_142588-143163 maize EST in NCBI using high similarity
    Found more than 25 hits e-value < e-30
    204g_expression confirmation_blast EST.JPG
     

    Conclusion

     

    204g region belongs to a catalytic/ protein phosphatase type 2C gene located in the genome:142588-143163 and coding for about 200aa. This result has been further confirmed through Maize EST database in NCBI.

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