MAIZE GENOME ANNOTATION PROJECTAGRY 60000GROUP 2

KARTHIK PADMANABHAN

SHUAI CHEN

SHAYLYN WIARDA

12/06/12

WORKFLOW1. 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 RESULTSExcluding Zea mays Zea mays alone

CPG ISLAND PREDICTION

GENE PREDICTION – RAW SEQUENCE

GeneMark FGENESH AUGUSTUS

Number of Genes 29 23 23

• 13 genes were common between GeneMark, FGENESH, and/or AUGUSTUS

REPEAT MASKER RESULTS

GENE PREDICTION – MASKED SEQUENCE

GeneMark FGENESH AUGUSTUS

Number of Genes 5 2 2

• No genes common between all 3• 1 gene common between FGENESH and

AUGUSTUS

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

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-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)• 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 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)• 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

GENE 5 (G, F)• 140856 to 141492 (8508-9144) 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:2.1.3.0,

F:kinase activity, amino acid binding, carbomyltransferase activity P: phosphorylation, cellular amino acid metabolic process