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Sequence 204 Gene Prediction 204i Evidence

     

    Summary

    This predicted protein (204i) matched to  MIF4G domain which is part of the  Pre-mRNA-splicing factor. The initial result shows 204i matched to the same group of reference protein as 204h. After look at the matches region by region, I found 204i matched to MIF4G domain and 204h matched to MA3 domain. After use a reference Sorghum gene blastn back to unmasked 204 genome sequence,  six trustable matches were found which can combined into two frames:

    1) 165990-167916 with + chain coding ~1200bp for ~400aa

    2)149006-152067  with - chain coding ~900bp for ~300aa 

    Frame one located in the same region of 204i coding MIF4G domain whereas frame two located in the same region of 204h coding MA3 domain. Considering the similar group of matched genes of 204i and 204h always have two domain at the same time and the similarity of the function of these two domains. I suggest to combine 204i and 204h into one whole  Pre-mRNA-splicing factor.

    This result has been further confirmed through Maize EST/cDNA database in NCBI.

     

    FGENESH predicted protein

    >FGENESH:   4   4 exon (s) 166294  - 168372   297 aa, chain +
    MRDRVSDDEKEEGRRRRRARDPDDEPDDRRGKRDREKDRRRHRRRSPSSESGSSPDGRRH
    RRRRRDEGSRRRDDRRRREDEGDERRRSPVKELTPPLPPPPPLLPEMIPGRTGGIYIPPF
    RMAQMMRDMEDKSSPEYQRLTWDALKKSINGLVNKVNATNIKNIVPELFAENLVRGRGLF
    CQSCIKSQMASPGFTDVFAALVAVVNTKFPEIGKLLLVRVVLQLKRAYKRNDKPQLLAAT
    KFIAHLVNQVVAHELVALELLTVLLENPTDDSVEVAVGFVKECGAMLQDLSPQGLHG

    GeneMark predicted protein

    >seq204 1600001-2000000 Xiaoqing Yu 09-16-2010_9|GeneMark.hmm|gene 9|367_aa
    MGNLSLGGSGVRTTPRRGRGRDAKPSEEKENGHAKPGRDEDGDNRSPRRDRVSDGEEGGE
    RRRMRDRVSDDEKEEGRRRRRARDPDDEPDDRRGKRDREKDRRRHRRRSPSSESGSSPDG
    RRHRRRRRDEGSRRRDDRRRREDEGDERRRSPVKELTPPLPPPPPLLPEMIPGRTGGIYI
    PPFRMAQMMRDMEDKSSPEYQRLTWDALKKSINGLVNKVNATNIKNIVPELFAENLVRGR
    GLFCQSCIKSQMASPGFTDVFAALVAVVNTKFPEIGKLLLVRVVLQLKRAYKRNDKPQLL
    AATKFIAHLVNQVVAHELVALELLTVLLENPTDDSVEVAVGFVKECGAMLQDLSPQGLHG
    KLFQTIV


    Blast result of G model predicted protein

    This model is better. Matched to same group of proteins as 204h but 204h and 204i can not match to each other, so check details using one Sorhum gene (XP_002456069.1) as reference.
    204h matched to 528-746aa   MA3 domain
    204i matched to 107-404aa    MIF4G domain
    To further clarify, use this  Sorhum gene (XP_002456069.1) mRNA sequence blast the 204 unmasked genome sequence.
     204i-G-Blastp_NCBI.JPG

     

    Reference gene Sorhum  (XP_002456069.1) mRNA

    >gi|242053846|ref|XM_002456024.1| Sorghum bicolor hypothetical protein, mRNA
    ATGGCCGCCTCCGCCTCCGCCTCCCCGCCGCGCCACCGCCACAGCCACCGCGATGAAGTCTCCCCGCGCC
    GCCGCAAGCGCCGCGCGTCCCCGTCTCCGTCCCCACCCCGCTCACCATCTCCCGGCGTCGACGCGGACCG
    CCGTCGCAGATCTAGGGCTTCGCCGCCCGATTCCGACCACCGCGGCCGCCGCCGCGACGCCAAGCCCTCG
    GAGGAGAAGAACGGCCACGCCAAGCCCGGAAGGGATGAGGACGGCGACAACCACCCTCCCCGGCGCGACA
    GGGTTTCAGATGGGGAGGATGGTTTCCAACGCCGGAGGATGCGCGATAGGGTTTCCGGCGATGAGAAGGA
    GGAAGGCCGTCGGCACAGGCGTGCTAGGGATGCGGATGACGCGCCTGACTACCGCCGTGGCAAGCGAGAC
    CGGGAGAGGGACAGCCGGTGCCACCGCCGCCGGAGCCCTAGCTCGGAGTCAGGGTCCTCACCCGACGACC
    GTCGACACCGCCGCCGGCGCCGAGACGAGGGCTCCAGGCGGCGGGATGACCGCAGGCGAAGGGAGGACGA
    CGGAGACGAGCGCCGGAGAAGCCCTGTGAAGAGGGAGCCGACCCCGCCACTGCCTCCACCACCACCACTG
    CTTCCGGAGATGATCCCTGGCCGCACAGGTGGGATCTACATTCCGCCTTTCCGCATGGCGCAGATGATGC
    GTGATGTAGAGGACAAGTCGAGCCCAGAGTATCAGCGCCTCACCTGGGATGCTCTCAAGAAGAGCATCAA
    TGGGTTGGTGAATAAGGTGAATGCGACCAATATCAAGAATATAGTGCCGGAGCTCTTCGCAGAGAACCTT
    GTTCGTGGGCGGGGGCTCTTCTGTCAGTCTTGCATCAAGTCACAGATGGCCTCACCTGGGTTCACCGATG
    TATTTGCTGCGCTAGTTGCGGTTGTGAATACCAAGTTCCCTGAGATTGGGCGGTTGCTTCTTGTTCGTGT
    TGTGCTCCAGCTCAAGAGGGCATATAAGCGAAATGACAAGCCTCAATTGCTTGCGGCAACCAAATTCATT
    GCGCACTTGGTAAATCAGGTGGTGGCACATGAGCTTGTGGCGCTGGAGCTTCTTACTGTACTCCTGGAAA
    ATCCAACTGATGATAGTGTTGAGGTCGCTGTGGGGTTTGTCAAAGAGTGTGGGGCAATGCTGCAGGACTT
    GTCTCCTCAAGGGCTTCATGCTATTTTTGAAAGATTTCGAGGCATTCTACATGAAGGAGAAATAGACAAG
    AGAGTGCAGTTTCTTATTGAAGGCCTTTTTGCAATTAGAAAGGCTAAATTCCAGGGTTTCCCAGCCATCC
    GTCCAGAGCTGGATCTAGTGGAGCAGGAGGACCAGTTTACACATGAGATATCCCTTGAAGATGACCTAGA
    CCCTGAGACCAATCTAAATGTTTTCAGGGCAAACCCCAATTTTGTTGAAGATGAGAAGGCATATGAGAAT
    CTAAAGAGAAGCATCCTGGGAGCAGAGTCTTCTGAAGATGAAGAAGGATCAGATGCTGCTTCTGATGATG
    ATGAAGATGAGGAAGAATCCGATGAAGAGGATGAGGAACAAATGGAGATAAGGGATAGAACAGAGACGAA
    TCTTGTGAACCTTAGAAGAACAATATATTTGACTATTATGTCCAGTGTTGATTTTGAAGAAGCTGGGCAC
    AAGCTTATGAAAATTAAGCTTGAGCCTGGTCAAGAGATGGAGCTGTGCATTATGCTTCTTGAGTGTTGCA
    GTCAGGAGAGAACATATCTTCGTTATTATGGGCTGCTAGGACAGCGATTTTGCATGATCAATAAAGTGTA
    CCAAGAGAACTTTGAAAAATGCTTTGTGCAACAATATTCGATGATTCATCGTCTTGAAACAAACAAGTTG
    AGGAATGTTGCCAAGTTCTTTGCACATTTGTTGGGGACTGATGCGCTCCCTTGGCATGTTTTGGCTTACA
    TCAGGTTGACAGAGGAAGACACGACATCATCTTCTCGAATTTTTATAAAAATTCTATTCCAAGAATTATC
    GGAGCACCTGGGCATACGCCTACTCAATGAGAGGCTGAATGATCCTAACATGCAAGGTTCCTTCGAATCT
    ATCTTCCCAAAGGATCATCCAAAGAATACAAGGTTCTCAATCAATTTCTTCACGTCCATTGGTCTTGGTG
    GTATAACGGAAAGCCTGAGGGAGTACTTGAAGAACATGCCGCGCCTAATAATGCAGCAGCAGAAGCCGGA
    ATCATCGCAGTCAGAATCAGGTGGATCTGAATCTGGTTCAGAATGCTCTAGCTCAGGGTCTAGTTCTGAG
    TCTGAGTCAGAATCAAGCTCTGATGAGAGTGACAGGAGGCGGAGTAAGAAGAGGAGGAAGAGGACTTG
     
     

    Blast back to 204c unmasked

    204i-reference-Blastn-back to-unmasked 204sequence.JPG
     Matched regions:
    15-1020 V.S. 165990-166992
    1019-1145 V.S. 167631-167757
    1142-1213 V.S. 167845- 167916

    1478-1716 V.S. 152061- 151760

    1715-2026 V.S. 149764-149453
    2012-2378 V.S. 149372- 149006

    Combine:

    165990-167916 (1926) =(1200bp/400aa 1-400)+ chain = 204i =MIF4G domain
    149006-152067 (3061) =(900bp/300aa 490-790)- chain =204h =MA3 domain
     

    Expression confirmation


    Genome DNA unmasked blast maize EST, input area 165990 to 167916 
    Matched to a lot of cDNAs, combine them together, I got 1-837 corresponding to 204 genome region: 165990-166827, 837bp
    204i_Expression confirmation-Blast EST.JPG

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