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Group 6, Gene III

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    Gene III was predicted by both GeneMark and FGENESH. GeneMark predicted that the gene had 2 exons (90,198-92,108 and 93,321-93,372) and FGENESH predicted that the gene had 1 exon (from 90,198-92,897). We ran a nucleotide BLAST search in the refseq_rna database using both predictions and found that the FGENESH prediction gave better hits. We concluded that FGENESH made a better prediction of this gene and based our gene model on the FGENESH prediction.

     

    Gene III Model:

    -predicted identity: 1,4-alpha-glucan-branching enzyme 3 / starch branching enzyme III

    -protein features: soluble protein

    -number of exons: 1

    -bp range: 90,198-92,897 in group 6 sequence

    -exon 1: 90,198-92,897

    -starts with start codon: Yes

    -ends with stop codon: Yes

    -all splice sites appear correct: N/A

    -nucleotide sequence:

    -start codon in green, stop codon in red

    ATGGCCTCGTGCCCTCTGTTCCTCCTTGTCCCGCGGCCCCCTCCTTCCCTTGT
    CGGCGCCGACCGCTGCCCAGGCTCCGCGGGCTGCTCAGATCTCCCAACTA
    GCTGCCGTCCTCATCCTGGACGCCGGCATGGTTACCCATTTCGTTGCAAC
    TCGTCTTCTTCCTCGTCCGCGCCTCGCGAGCGCCCGCCCAGGCAGCGCCC
    CGGTGGCCGTGGCGACGCCATCGACCCCGTAGGCTTCCTCACCAAGCTCG
    GCGTCTCGGACCGCGCCTTCGCCCAGTTCCTCCGCGACCGGCACAAGGCC
    TTGAAGGACCGTAGATGGGAGCTGTGTTCTCGGTTTATTGATCTGAAAGA
    GGCATCTTCTGGGTTTGAGTTATTGGGCATGCACCGACATCGACAACACC
    GCATCGATTTCATGGAATGGGCTCCAGGTGCTCGGTATTGTTCTTTGATT
    GGTGATTTTAATCAGTGGTCGCCAACTGAAAACTGTGCCAGGGAAGGTCA
    TTTAGGACATGATGATTTTGGATATTGGTTTATCATACTTGAAGATAAGC
    TCAGAGAAGGGCAAGAACAAGATGAATATTTCTTCCAGGAATACAATTAT
    GTGGATGACTATGATAAAGGTGACAATGGCATTGATGCTGATGAAATAAT
    GCGTAGGATGAAAGAAGAGTATTGGGAACCTGGAGAAATCAGGTCCCGTC
    AGTCTCAGTTAGAGATGGTTGTTAAGCTATATGAGCAAATGTTTGGCCCA
    AACGGTCCACAAACAGAGGAGGAGCTAGGTGAAATTCCTGATGCCCAAAC
    AAGATACAATGAGTTCAAAGCATCGCAGAAGGCTGACTCTTCCAGCCAGC
    CTTCCTATGATATCATTGACAATGGGCAGGAGTTCGACATTTTCAGTGTT
    GTAACTGATCGTGCATCATTTGAAAAGTTTCAAGCAAAAAAACCTCCCCT
    TGCTTACTGGGTTGAAATGAGGAAAGGTCGAATAGCATGGCTTGAGAAAT
    ATGTTCCAACAATTTCTCATAAAGACAAGTACAGGGTTTATTTTAATACT
    CCTGATGGTGCTTTAGAACGTATTCCTGCTTGGGCTGCATATGTTCTTCC
    AGATGCTGAGGGGAAGCAATCCTATGCAGTACATTGGGAACCACCTCCTG
    AAGAAATTTACAAATGGAGATTTGGACGTCCAAAGGTGAAGGGTTCACTT
    AGAATATATGAATGTCATGTTGGAATAAGTGGTTCAGAGCAAAAGGTTTC
    ATCATTTCAGGAGTTCACATCCAAAGTCCTACCGCATATAAAAAAAGCTG
    GATATAATGCTGTTCAGCTGATTGGTGTTGTGGAGCACAAGGATTACTCC
    TCCATTGGCTATAAGGTCACTAATTATTTTGCAGTCAGCAGCAGATTTGG
    CACCCCAGATGACTTCAAGAAATTAGTCGATGAAGCGCATGGCCTTGGAT
    TAGTAGTGCTTCTGGATATTATCCACTCCTATGCATCCGCAGATGAACTG
    GTTGGCTTATCACTTTTTGATGGCTCTAATGACTGTTACTTCCACAGTGG
    AAAAAGAGGGCATCACAAGTACTGGGGCACCAGGATGTTTAAATATGATG
    ATGTGGATGTTCTGCACTTCTTGTTGTCCAATTTGAATTGGTGGGTCACT
    GAGTACCGGATTGATGGATTCCAGTTCCATTCCTTGTCTTCTATGTTATA
    TACTCATAATGGGTTTTCTACTTTTACTGGTGCCATGGAAGAGTATTGCA
    ATCAGTATGTTGACAAGGATGCACTGATATATCTAATTCTAGCAAATGAA
    ATGTTACATCGTCTTCATCCAGATATTGTAACAATTGCTGAAGATGCAAC
    ATTTTATCCTGGATTATGTGAGCCAATTACTCAAGGCGGATTGGGATTCA
    ACTACTGGGTCAATCTTTCTATACCAGAAATGTGGTTGTGGCATCTTGAA
    AATGTCCCTGAACAAGAATGGAGCATGAATAAGATTATTAAAGTATTAGT
    AAGCAGTAACCAGAATATGCTATCATATGTTGAAAATCATAACCAGTCCA
    TATCTGGACGCAAGTCTTTTGCTGAGATAATTCTTAATTCAAGAGAGTGC
    TCTGTTGGTTCTGTTGACGACAATTTGATTAGAGCTTCTTCTTTGTTGAA
    ATTGATGAAACTAATTACTTTCACGACAAGCGGAGGCGCTTATCTCAACT
    TCATGGGCAATGAATTTGCACATCCAGAAAAAGTTGAATTTCCTATGCCA
    AGCAATGACTATTCCTTCGAGTTAGCTAATCGGCAATGGGAACTATTGGA
    CAAAGTTTTTCATAAACATATATTTAACTTTGACAAGGATGTTATGAGCT
    TGGATGAAAATGAAAGGATAATTTCTAGAGGTCCACCCAACATTCTTCAC
    TGTGATGACACAAGCATGGTCATATCTTTCACAAGAGGGCCTTTATTTTT
    CATATTTAATTTTAATCCTCAAGTCTCCCATCAGTCGTATCGTGTTGGTG
    TGGATGAAGCTGGGGAATACCAACTCATCTTCAACACAGATGAAACTAAA
    TATGGTGGATGTGAAACCCTCAAGAGTAGTCAGTATATGCGGAGGACCTC

    TGATAAAAGAGCTGATGGTTGTCGCAACTCCTTGGAATTGGCATTGCCAT

    CTAGAAGTGCTCAGATTTACAAGTTAGTTAGAATTTTGAGAATTTAG

    -amino acid length: 899

    -amino acid sequence:

    MASCPLFLLVPRPPPSLVGADRCPGSAGCSDLPTSCRPHPGRRHGYPFRCNSSSSSSAPR
    ERPPRQRPGGRGDAIDPVGFLTKLGVSDRAFAQFLRDRHKALKDRRWELCSRFIDLKEAS
    SGFELLGMHRHRQHRIDFMEWAPGARYCSLIGDFNQWSPTENCAREGHLGHDDFGYWFII
    LEDKLREGQEQDEYFFQEYNYVDDYDKGDNGIDADEIMRRMKEEYWEPGEIRSRQSQLEM
    VVKLYEQMFGPNGPQTEEELGEIPDAQTRYNEFKASQKADSSSQPSYDIIDNGQEFDIFS
    VVTDRASFEKFQAKKPPLAYWVEMRKGRIAWLEKYVPTISHKDKYRVYFNTPDGALERIP
    AWAAYVLPDAEGKQSYAVHWEPPPEEIYKWRFGRPKVKGSLRIYECHVGISGSEQKVSSF
    QEFTSKVLPHIKKAGYNAVQLIGVVEHKDYSSIGYKVTNYFAVSSRFGTPDDFKKLVDEA
    HGLGLVVLLDIIHSYASADELVGLSLFDGSNDCYFHSGKRGHHKYWGTRMFKYDDVDVLH
    FLLSNLNWWVTEYRIDGFQFHSLSSMLYTHNGFSTFTGAMEEYCNQYVDKDALIYLILAN
    EMLHRLHPDIVTIAEDATFYPGLCEPITQGGLGFNYWVNLSIPEMWLWHLENVPEQEWSM
    NKIIKVLVSSNQNMLSYVENHNQSISGRKSFAEIILNSRECSVGSVDDNLIRASSLLKLM
    KLITFTTSGGAYLNFMGNEFAHPEKVEFPMPSNDYSFELANRQWELLDKVFHKHIFNFDK
    DVMSLDENERIISRGPPNILHCDDTSMVISFTRGPLFFIFNFNPQVSHQSYRVGVDEAGE
    YQLIFNTDETKYGGCETLKSSQYMRRTSDKRADGCRNSLELALPSRSAQIYKLVRILRI-
     

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