MAIZE GENOME ANNOTATION PROJECT AGRY GROUP 2 KARTHIK PADMANABHAN SHUAI CHEN SHAYLYN WIARDA 12/06/12

WORKFLOW 1.MegaBLAST 2.Gene Prediction on unmasked sequence AUGUSTUS FGENESH GeneMark 3.CpG island prediction 4.Repeat Masker 5.Gene Prediction on masked sequence AUGUSTUS FGENESH GeneMark 6.BlastX against protein database 7.BlastN against EST database 8.Pfam 9.Blast2Go

MEGABLAST RESULTS Excluding Zea maysZea mays alone

CPG ISLAND PREDICTION

GENE PREDICTION – RAW SEQUENCE GeneMarkFGENESHAUGUSTUS Number of Genes genes were common between GeneMark, FGENESH, and/or AUGUSTUS

REPEAT MASKER RESULTS

GENE PREDICTION – MASKED SEQUENCE GeneMarkFGENESHAUGUSTUS Number of Genes 522 No genes common between all 3 1 gene common between FGENESH and AUGUSTUS

GENE 1 (A, F) ( ) on the minus strand 77% match to hypothetical protein [Zea mays] GenBank: ACG with an e-value of 5E-120 EST evidence : 1 exon with >5 ESTS with >95% identity Pfam: no results Blast2GO: no results

GENE 2 (A, F, G) ( ) on minus strand 52% match to uncharacterized protein LOC [Zea mays] with an e-value of 2E-88 5 exons, EST evidence has evidence for 2: Pfam: Seryl-tRNA synthetase N-terminal domain match with E- value of 0.45 (insignificant match) Blast2Go: F: Zinc ion binding, C: intracellular

GENE 3 (A, F, G) to ( ) 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 GTPase activity 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

GENE 4 (G) to 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

GENE 5 (G, F) to ( ) on minus strand 91% match to ornithine carbamoyltransferase [Zea mays] 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: , F:kinase activity, amino acid binding, carbomyltransferase activity P: phosphorylation, cellular amino acid metabolic process