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Group 6

Group 6. Bikash Shakya Emma Lang Jorge Diaz. Sequence 6. BLASTx entire sequence against 9 plant genomes. RepeatMasker  55.47 %  repetitive  sequences 82.5 % retroelements 13.0 % DNA transposons EMBOSS explorer 74 CpG islands 54 inverted repeats. GENE PREDICTION.

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Group 6

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  1. Group 6 BikashShakya Emma Lang Jorge Diaz

  2. Sequence 6 • BLASTx entire sequence against 9 plant genomes. RepeatMasker •  55.47% repetitive sequences • 82.5% retroelements • 13.0% DNA transposons EMBOSS explorer • 74 CpG islands • 54 inverted repeats

  3. GENE PREDICTION 7 most promising genes Bases: •START & STOP codons •High GC content •No repeats •Good E-value •Proper splice sites•Both program agreed •No mobile elements

  4. Final Gene Model PredictionFour genes: I, II, III, IV GENE I: Zea mays uncharacterized protein LOC100194332 Both programs predicted the exact same 3 exons RNA Evidence • BLAST search in the refseq_rnadatabase • Zeamays uncharacterized LOC100194332 (LOC100194332), mRNA(cDNA) Identity:100% E-value:0 Sequence alignment with the translated sequences

  5. GENE I Perfect match

  6. EST Evidence Identity:99% E-value:0.0. EST data covered both exons 1 & 2 except 114 bases GENE I Protein function • Conserved domain: Myb DNA binding • Predicted to be a MYB related transcription factor • Myb proteins bind to DNA and regulate gene expression

  7. Gene II • 6 exons • 241 amino acids • membrane protein with 7 transmembrane helices • sugar efflux transporter Image from: http://bp.nuap.nagoya-u.ac.jp

  8. Gene II RNA and EST Evidence • 99% match to “Zea mays seven-transmembrane-domain protein 1” (LOC100284352) mRNA (cDNA) • EST data covered all of exons 1, 2, 3, and 4 plus beginning of exon 5 • All EST sequences used had 98-99% identity with gene II

  9. GENE II Protein Function • conserved domain: MtN3_slv • Sugar efflux transporter • Involved in seed and pollen development

  10. Gene III • 1 exon • 899 amino acids • Soluble protein • 1,4-alpha-glucan-branching enzyme 3/ starch branching enzyme 3 • Matched orthologsin 5 other plant genomes. Starch branching enzyme I from rice. Image from: http://pdb.rcsb.org

  11. Gene III RNA and EST Evidence • 99% match to “Zea mays starch branching enzyme III (sbe3)” mRNA (not cDNA) • EST data covered almost all of gene III (1 gap) (intron?) • All EST sequences used had 99%-100% identity with gene III

  12. Segment without EST data aligns to starch branching enzyme III in A. thaliana – not an intron

  13. GENE III Protein Function • conserved domains for 1,4-alpha-glucan-branching enzyme • top HHpred result was starch branching enzyme 1 in rice (e-value: 2e-128) • These enzymes catalyze the formation of the alpha-1,6-glucosidic linkages in starch.

  14. Gene IV • 5 exons • 583 amino acids • Membrane protein with 10 trans-membrane helices • Amino acid transporter • Matched orthologs in wheat and sorghum genomes.

  15. Gene IV: RNA Evidence • 96% match to “Zea mays LOC100193963 (si486073c04), mRNA” (E=0.00) (not cDNA) • Other good match was to “XM_002455881.1Sorghum bicolor hypothetical protein, mRNA” (94%, E=0.0)

  16. Gene IV: EST Evidence • EST best matches: • ZM_BFc Zea mayscDNA clone ZM_BFc0171C07 5‘ (95%, E=0.0) • ZM_BFc Zea mayscDNA clone ZM_BFc0038P24 5‘ (96%, E=2e-158) • EST data also have two gaps.

  17. Gene IV: BlastX in Nov. 2012

  18. GENE IV: Protein Function • Conserved domains: • NCBI BlastX • InterProScan

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