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Sequence 204 Gene Prediction 204k Evidence

     

    Summary:

    Based on the evidence listed below, I think this is a putative FAR1 or transposase gene located in the genome area 225159-228046 coding about 440aa.

    This result have been confirmed through Maize EST/cDNA database in NCBI, however, the evidence for this gene is not as strong as others. See expression confirmation for details.

    GeneMark Prediction

    >seq204 1600001-2000000 Xiaoqing Yu 09-16-2010_11|GeneMark.hmm|gene 11|64_aa
    MGDVIMSCHWLERGALFSTDRRRQLGSIVITLAHIYRNNLESTTRGDLSPTSRQQAPGVW
    LVDL

    Blastp

    no any matches.

     

    Expanded sequence (+1000 in upper and lower) Masked  

    >seq204 1600001-2000000 Xiaoqing Yu 09-16-2010 [Using bases 225021 to 231090 ]


    Blastn in flowering plants result

    Region 1760-2119 (Genome Location: 225021+1760=226781-227140 = 359bp =119aa) Matched to rice sorghum

    Matched to  the middle of a gene of rice in the area 4271-4624
    204k_Genome expanded_blast.JPG
     

    Matched rice gene

    >(gi|62543365:<77-190, 303-386, 956-1028, 1109-1195, 1283-1337, 1427-1498, 1890-1952, 2060-2174, 3470-3533, 3630-4868, 5212-5846, 5937-6095, 6201-6308, 7488-7961) Oryza sativa Japonica Group chromosome 10 clone OSJNBa0062C05 map S21174S, complete sequence
    GGACTTATTACCAAATCCAGAAAGGGCCTGGATCCTGCAGTTGCTCGCTATGCCAGAGGTTTTGGTCCTG
    AAGAGGTGCAAGATCTCCATGAGGGGGCTAGTCTTGTTGAAGTGCTTTATACTGATCATCAGGTCAGGAA
    AGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAGGTTCTCAAGGCT
    ATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCAATGTCCAACCCAACTACTAAAGCCGAATGTA
    CTCCTGAAGATGTATTCAAATATGTTGGAGACAATGCAGTATTTGCCAGTGGAAGCCCTTTCAGTAATGT
    CACTTTAGGCAATGGTAGACAAGGGTACGCTAATCAAGCAAACAATATGTATCTGTTTCCTGGTATCGGT
    TTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTGCCTTG
    CGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAGTATCAGGCACAT
    CACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGTTGATGAAGATCTGGCCGAGGGGCGTTGTGAT
    GTAGACGCTAGGGACCTCAAGAGCATGACTGAGTGTTGGAATAATTCATCAAAGAAGCCTCCAGCAAAAT
    CTGCATATTTGAGATGGAAGAAAACAGTGGGTGTGCTACCTAGTTTGTTACCTGAAGTTGGCATGGAATT
    CAATACTGTTGATGAGGCTTGGATGTTTTGGGTTAGCTATGGTGGTCAAAAAGGTTTCGAGGTTAGAAAA
    AGGTACTCAAACAAAAGGAAATCAGATGGAAAGGTTAGGTCATGCAGATATGTTTGTGCAAATGAGGGTC
    ATAGAAAGGAGGATAAAAGGGATCATCTAACAAAGTGTCCAAGAGCTGAAACGAGAACCGATTGTCAAGT
    TCGCATGGGTGTTGTGCTAGATCAGGAGAAAGGGAATTATAAAGTGGCTGATCTAGTTTTGGAACACAAT
    CACATCCTTCAATTGCCAGAAACCTCGCACTTGATGGTGTCTCAAAGGAAAATTTCAGAGTTACAAGGTT
    TTGAAATTGAGACAGCTGACGATGCGGGCATTGGGCCCAAAGCAGCACATCAGTTGGCTAGTATCCAAGT
    TGGTGGCTCACTTAATCTCAATTGCACTCTCCGTGACCACAAGAATTATTTACGGGGCAAACGCCAACGA
    GAGATGGTATATGGTCAAGCAGGAAGCATGCTCATGCATTTTCAAGATAAAATTGCTGAGAACCCGTCAT
    TTCAATATGCATTGCAGATGGATAGTGAGGAGCAAATAGCAAACATATTCTGGGTTGATGCTAAAATGCT
    CACTGACTATGCATATTTTGGTGATGTTGTCAGTTTTGACACTACTTTTGGAACAAACAAGGAAAGTAGG
    CCTTTTGGTGTATTTGTTGGGTTCAATCAGTTTAGGGAAACAATGGTTTTTGGTGCTGTTCTACTGTATG
    ATGAGACATATGAGTCCTTCAAGTGGTTATTTGAGACCTTCCTAAAAGCACATAATGGCAAGCAACCTAA
    AACAATCTATACTGATCAGGATTCTGCAATGGGAAAAGCAATTAAGAAAGTGTTTTTAGAATCATGGCAT
    GGTTTGTGCACTTTCCATATCATGCAGAATGCTGTTAAACATGTAGCTGAACTCGAGGATGAAGAATCCA
    GTAATTCTCCCAAACAGACTGCCGAAGATAACGAGGAAGAACGAAGTATTCTCGCAGATTTTAGTGCATG
    TATGTTTGAGTACGAAGATGAGGAAACATTTGAACAAGCATTTAGCACCATAAGGGCAAAGGCGAGCAAG
    CAAAGTTGGTTGGATAGTATATACAAGGTGAAAGAAAAATGGGCTGAATGTTACATGAAGGATGTGTTCA
    CATTAGCATGCACCACGGCATTGGAAGGCAACAATTGCTATCTTGTGGCAATTGGCAGTCTAGATGAAAA
    TTGTACCTTTGAGAAGGAGTACAAAGTTGTTGGTGATCCTTTAGAGCAAACTAGTACATGCGGCTGTGGG
    ATGTTCAGTAGAACTGGAATATTGTGTGCACATGCTTTAAAAGTCCTTGATTTGATGAATATAAAATCTC
    TCCCATCACAATATGTACTGAAGCGATGGACACGTGGAGCACATAGTGGGACAGTACAAGATAACCATGG
    ACGAAGTATTATAGAGAACCCAAGATTAAATGAGATGCTTCGCTACAAAGATATGACCCGCAAATTTCTC
    AATTTGGCACTTCGAGCTGCCAGCCATCCAGGGTCTACCTTGTTAGTAAACAACGCACTTGATATCCTTA
    GCAAGCAAGTTGAAGAAGAAATCAATGGATTTACTGATACCATAGCTCTAGGTCCCACTGATATTACTCC
    TCCAAGTGACTTGGTGAGTACAGCTCGCCTAAAGAAAAAGGAGGTGGAAACAAAAACCTCAAAGCGCAAA
    AAAAATTGGCTTGATAAGCTGCACAAGTCCACAAAGAATGGAAGTAACAAGGGAGGTAAGAGAAAGAAAA
    AAGGTTCAAAGGAACAAAAGACTGCAAAGACGGGAGGCAAGAAAAAGGGAAAAGAAGCATCAGTACATGA
    CAATCCAGCAGGGCAAAATATATATCCTAGTACCTCTTTGCCCATGGAAGAAATGTCTGAACCATACATG
    GCCATCAACACCTTCTCTCAACTATTGACGCAATGGAGTTTGGTTTTGGTGAATAGGCTTTTGGTCTCTG
    CGGGCTGCGGCACCTGCCGAGATTGTTCTTTTGGCACGCTTGATGAACAGCTTGATCTTTTGGGCAAGAG
    CAAGGTTGACTGGTTGAGCGGGGTGGAGGCGACAGGCGGGGCGGAGCTGGACGGGCGGTGGCCGGAGCAG
    GCCAGTGGAGCTAAGCGGCGGTGGCCGGAGCAGGGGCAAGGGGCCACGGCACCGCGATGCCGAGGGGTGA
    CTGGCGGAGAGAGGGGCGGCGGGTGGAGCAGTGGAGAGTGGCGGCGAGCTCCTGGGAGATGGCGACGGGA
    TGAGGCCGAGAGGACGCCAACGGCGAGGTGGAGCACGCACCTCAAGAAGCGGGTGTCGCCGGAGCAGAAG
    AAGGGTGGGGGCAAGAGCAAGAAGAAGATGACCTGGACCGACGTGCTCGTCCCGTCCCCCTCGCCATCGT
    CATCCTCCACCGCGACGACCAACTGCTCCAGGCTCCAGCGGCGACTCGGCCGATGCGCAGAGCAACACAA
    GCAAGGAGGAGGAGGCGGACAAGATCGAGATCCCCATGCTCGACCCCTGTAG

     

    Blast this rice gene back to 204 genome (unmasked) sequence

    204K_rice blast back to genome.JPG
     
    Four matches found: 226779-227310, 225195-225362, 226553-226777, and 227907-228046

    In the area of 225159-228046=2887bp
    Rice query: 840-2270=1430bp coding 440aa (from 280 to 720aa), 1430bp out of 3342 bp = 43% DNA sequence matched

    Using the protein sequence of this gene blast protein database  

    The matched area matched to a transposase protein in rice and Sorghum.  E=0!
    Those genes commonly contain two to three domain:
    One is FAR1 DNA-binding domain (266-354) and the other is MULE transposase domain (481-571)
    The last one usally is SWIM zinc finger but our genome sequence coding area do not contain this part.

    204K_rice_protein_blastp_NBCI.JPG

     

    Expression confirmation

    Genome DNA unmasked blast maize EST
    Using sequence 204_ 225159-228046 maize EST in NCBI using high similarity

    Only one match found

    204K_expression confirmation Blast maize EST.JPG
     

    Lower the standard, using 'Somewhat similar sequences' found many matches 

    204K_expression confirmation_lower similarity.JPG
     

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