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Maize genome annotation project Agry 60000 group 2

Maize genome annotation project Agry 60000 group 2. Karthik Padmanabhan Shuai Chen Shaylyn Wiarda. 12/06/12. workflow. MegaBLAST Gene Prediction on unmasked sequence AUGUSTUS FGENESH GeneMark CpG island prediction Repeat Masker Gene Prediction on masked sequence AUGUSTUS FGENESH

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Maize genome annotation project Agry 60000 group 2

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  1. Maize genome annotation projectAgry 60000group 2 Karthik Padmanabhan Shuai Chen Shaylyn Wiarda 12/06/12

  2. workflow • MegaBLAST • Gene Prediction on unmasked sequence • AUGUSTUS • FGENESH • GeneMark • CpG island prediction • Repeat Masker • Gene Prediction on masked sequence • AUGUSTUS • FGENESH • GeneMark • BlastX against protein database • BlastN against EST database • Pfam • Blast2Go

  3. MegaBlast Results Excluding Zea mays Zea mays alone

  4. CpG Island Prediction

  5. Gene Prediction – RAW sequence • 13 genes were common between GeneMark, FGENESH, and/or AUGUSTUS

  6. REPEAT MASKER RESULTS

  7. Gene Prediction – masked sequence • No genes common between all 3 • 1 gene common between FGENESH and AUGUSTUS

  8. GENE 1 (a, F) • 10175-11176 (138824-139825) on the minus strand • 77% match to hypothetical protein [Zea mays] GenBank: ACG42783.1 with an e-value of 5E-120 • EST evidence : 1 exon with >5 ESTS with >95% identity • Pfam: no results • Blast2GO: no results

  9. Gene 2 (A, F, G) • 32122-34481 (115519-117878) on minus strand • 52% match to uncharacterized protein LOC100382558 [Zea mays] with an e-value of 2E-88 • 5 exons, EST evidence has evidence for 2: • Pfam: Seryl-tRNAsynthetase N-terminal domain match with E-value of 0.45 (insignificant match) • Blast2Go: F: Zinc ion binding, C: intracellular

  10. Gene 3 (A, F, G) • 64694 to 71049 (78951-85306) on the minus strand • 100% match to SEY1 with an e-value of 1E-102 : generate and maintain the structure of the tubular endoplasmic reticulum network, has GTPaseactivity • Exons with good evidence • Pfam: Root hair defective 3 GTP-binding protein (RHD3): regulated cell enlargement, membrane trafficking • Blast2GO: P:root epidermal cell differentiation, cell tip growth, C: integral to membrane, ER F: hydrolase activity, GTP binding

  11. GENE 4 (G) • 139202 to 139814 on plus strand • 73% match to putative growth-regulating factor 1 [Zea mays] with an E-value of 1E-7 • 3 exons with good ESTs • Pfam: no hit • Blast2Go: no hit

  12. Gene 5 (G, F) • 140856 to 141492 (8508-9144) on minus strand • 91% match to ornithine carbamoyltransferase [Zeamays] with an e-value of 5E-33 • catalyzes the reaction between carbamoyl phosphate (CP) and ornithine (Orn) to form citrulline (Cit) and phosphate (Pi) • 2 exons with good EST evidence for both • Pfam: no match • Blast2Go: ornithine carbomyltransferase, EC:2.1.3.0, • F:kinase activity, amino acid binding, carbomyltransferase activity P: phosphorylation, cellular amino acid metabolic process

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