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Group 6, Gene II

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    Gene II was predicted by both GeneMark and FGENESH. GeneMark predicted that the gene had 6 exons (48,105-48,147; 48,284-48,320;  48,434-48,650;  48,758-48,919;  50,183-50,302;  50,421-50,575) and FGENESH predicted that the gene had 5 exons (47,729-48,147;  48,284-48,650;  48,758-48,919;  50,183-50,302;  50,423-50,575). We ran a nucleotide BLAST search in the refseq_rna database using both predictions and found that the GeneMark prediction gave better hits. We concluded that GeneMark made a better prediction of this gene and based our gene model on the GeneMark prediction.

     

    Gene II Model:

    -predicted identity: seven-transmembrane-domain protein 1 (sugar efflux transporter for intercellular exchange)

    -protein features: membrane protein with 7 transmembrane helices

    -number of exons: 6

    -bp range: 48,105 - 50,575 in group 6 sequence

    -exon 1: 48,105-48,147

    -exon 2: 48,105-48,147

    -exon 3: 48,434-48,650

    -exon 4: 48,758-48,919

    -exon 5: 50,183-50,302

    -exon 6: 50,421-50,575

    -starts with start codon: Yes

    -ends with stop codon: Yes

    -all splice sites appear correct: Yes

    -nucleotide sequence:

    - start codon in green, stop codon in red, introns in yellow 

    ATGATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCGGTA

    CGTTGGTTCAATCGGCGGCGCGCGCGTGGAACTCATTCTGGATCGAGCGG

    TTTTGGTTTGATATATATGATCGATTTCGCTGGGCGTCTCGATCGGGTGC
    TCACGCTTGGTTATTTTCTCGCTTTGGTTGCAGGCAATGTCATCTCCTTT
    GGCCTCTTCCTCTCCCCAGTGTAAGCACGGATCGATCCCTCCGCGTTTCG
    ACGAGCGAGCCTGGTGGTTTTAATTTGGTTAGGGTTTTGTTTGTGCTGAC
    GGAGAGGCGGCGCATGCATTTTTACCTGTGCAGTCTGACGTTCTGGCGGA
    TCTGCAAGGCCAGGGACGTGGAGGAGTTTAAGCCTGACCCCTACCTGGCG
    ACGCTGCTCAACTGCATGCTCTGGGTGTTCTACGGCATCCCCGTCGTCCA
    CCCTAACAGCATCCTCGTCGTCACCATCAACGGCGTCGGGCTCGTCATCG
    AGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGC
    GTGAGTGCCACGGCGATGGCGCTGCACAAATGCCGGCCGTGTGTTCCCTC
    TTCGGATCTAGTTTTGAGCTTGACGATCCCTTACGCCTTATTAATTCTCG
    TTCGCAGAGGAAAGCGTTCGGAATCCTGGCCGTGGAGATTTTGTTCATGG
    TCGCCGTGGTGCTTGGTGTGATTTTGGGCGCCCACACGCACGAGAAGCGC
    TCCATGATCGTCGGCATTCTCTGCGTCATTTTCGGCTCGATGATGTACGC
    CTCCCCACTCACCATTATGGTACGTGATCGATCATCTATCCGGCCTCTCT
    TTTACTGTGCCTGCCGGATTTTGCTGCTCAGTTGCGTGGATAACCTTTAC
    CGTCGTGGAGTAGATCAGGTTGCAATAATTAGGCAAGTGTTTATCTGCAT
    GGGTTTAATTCTGGGACCCACGTGTCGGTTGATGGTTGCGATATTTTTTA
    ATGGATATATGGATAGAAGTTACTAGTCCTGGGAGAAATCGAGGAGTGCG
    TGCCTAATTTGGTTGGCGGCTGCGGCGGCCGCGATGCGGGGTAGATTAAT
    CTGGTTTCCATGGTCACTCACTGTTGGGCTGGGGAAGGATTTGGTGGACC
    TACTTGCCAGTGAACTGTTACCTTTGCCGGCTAGTGGTTGTACTGGTTTC
    TGTGTGTTCAGGTGTTTCACTGTTTATATTTGAACTTCTGGAACCATGCG
    AGAGGATTAGACTTCTTCTCCAGGTCATGCATGTAAACTTATTAGCTTTA
    ATCCATTGCTAATTGGTCAAGAGTTCCAATCTTCGTTAAAACTTTTGAGC
    ATGATCACCTTTATAACTTGTTGCATGACCTAGATCTGTTAAGGATTTTG
    CAGCGTGCACAGATGATCCATCATAGTACGTGTGGCATGTAATTGAGTCG
    ATAGCAGCACAGCTTGGTTGTTTATCTTGGATGACAACAGATGAGAAAGC
    CAATTTCGTTTAAAGTATCTAAAAGTTGCATGTATTAATGCCCACGTTTG
    GCGTTTAGATCTTGTCAAATATTTCTCCTGGGGTACAAAACAACGTGCCC
    CCGGCCGCTTAGTCAAATTGTCTTTTGTATAATTCCTCCTTGACACCTTT
    ATCTCCGTCAAAAAGGCTTACTGTATTTACTGACTAGCTAGCTAACTACG
    GTGTTGCCAGCTCGTTCACCTGGTGCTTTCATTCCATAGTTAGTAGGTTG
    TTTCTTTGCTGTGCATTGGCTTGACAAACCACATACCAAACTTGTTCAGT
    TGCGCTCACCTAACTCGCGTGGTGCTAACGTGACGGGTCTGGACGCAAAG
    AATCTGGCGGGCAGTTACATTTTATGGCAAAATAAACGTATGCCGCCGCT
    TGATCAATCTTGTGTGCCAGTTTCGGGTGTGATAGTTTTGGAATATATTG
    TTCCTGCAATCTGTTGCGCTTTCTGTTTCACACTCCGATTCGAAACACAG
    TGAAAATGTTTCTATCCTTGGATGGATCTAAGCTATTTGGGCAGATGTGA
    ACTTGTGATCTTTTTTTTTTTTTTTGGTGCAGAGCCGTGTGATCAAGACC
    AAGAGCGTTGAGTACATGCCCTTCCTCCTCTCGCTGGTGAGCTTCCTCAA
    TGGCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTTA
    CGGTCAGTATCGATCGCCTATGAATTTGCATGCGTCTCTTCTCCACATGT
    AACAAAAGCGTTACAGAATTCCATCTCTAGGTTGAGTAGAATCTCAGTTA
    TTAATAAATACCTGCAATGCAGATCCCCAACGCCCTTGGCGCCTTCTTCG
    GTCTCATCCAGCTAATCCTCTACTTCTGCTACTACAAGTCGACCCCCAAG

    GAGAAGAATGTGGAGCTGCCCACCGTCTCCAGCAACGCCGGCGGCGGCAA

    CGTCACCGTCAGCGTCGAGCGATAG

    -number of amino acids: 241

    -amino acid sequence:

    MISPDAARNVVGIINVISFGLFLSPLTFWRICKARDVEEFKPDPYLATLLNCMLWVFYGIPVVHPNSI
    LVVTINGVGLVIEAIYLTIFFLYSDGPKRRKAFGILAVEILFMVAVVLGVILGAHTHEKRSMIVGILCVI
    FGSMMYASPLTIMSRVIKTKSVEYMPFLLSLVSFLNGCCWTAYALIRFDLYVTIPNALGAFFGLIQLILY
    FCYYKSTPKEKNVELPTVSSNAGGGNVTVSVER

     

    Note: The reading frame for each exon was chosen based on alignment to the amino acid sequence of seven-transmembrane-domain protein 1 (LOC100284352) from Zea mays (ref|NM_001157247.1|).  
     

     

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