1. Bikash Shakya Emma Lang Jorge Diaz

2.  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 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

4. GENE I: Zea mays uncharacterized protein LOC100194332 Both programs predicted the exact same 3 exons RNA Evidence  BLAST search in the refseq_rna database  Zea mays uncharacterized LOC100194332 (LOC100194332), mRNA (cDNA) Identity:100% E-value:0 Sequence alignment with the translated sequences

5. GENE I Perfect match

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

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

10.  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: http://pdb.rcsb.org

11.  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.  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.  5 exons  583 amino acids  Membrane protein with 10 trans-membrane helices  Amino acid transporter  Matched orthologs in wheat and sorghum genomes.

15.  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 )XM_002455881.1

16.  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.

18.  Conserved domains: ◦ NCBI BlastX ◦ InterProScan