Bikash Shakya Emma Lang Jorge Diaz.  BLASTx entire sequence against 9 plant genomes. RepeatMasker  55.47% repetitive sequences  82.5% retroelements.

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Presentation transcript:

Bikash Shakya Emma Lang Jorge Diaz

 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 Masked sequence GeneMark 12 genes FGENESH 10 genes Unmasked sequence GeneMark 27 genes FGENESH 28 genes BLASTx 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

GENE I: Zea mays uncharacterized protein LOC Both programs predicted the exact same 3 exons RNA Evidence  BLAST search in the refseq_rna database  Zea mays uncharacterized LOC (LOC ), mRNA (cDNA) Identity:100% E-value:0 Sequence alignment with the translated sequences

GENE I Perfect match

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

 6 exons  241 amino acids  membrane protein with 7 transmembrane helices  sugar efflux transporter Image from:

 99% match to “Zea mays seven-transmembrane- domain protein 1” (LOC ) 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

 conserved domain: MtN3_slv  Sugar efflux transporter  Involved in seed and pollen development

 1 exon  899 amino acids  Soluble protein  1,4-alpha-glucan- branching enzyme 3/ starch branching enzyme 3  Matched orthologs in 5 other plant genomes. Starch branching enzyme I from rice. Image from:

 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

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

 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.

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

 96% match to “Zea mays LOC (si486073c04), mRNA” (E=0.00) (not cDNA)  Other good match was to “XM_ Sorghum bicolor hypothetical protein, mRNA” (94%, E=0.0 )XM_

 EST best matches: ◦ ZM_BFc Zea mays cDNA clone ZM_BFc0171C07 5‘ (95%, E=0.0) ◦ ZM_BFc Zea mays cDNA clone ZM_BFc0038P24 5‘ (96%, E= 2e -158 )  EST data also have two gaps.

 Conserved domains: ◦ NCBI BlastX ◦ InterProScan