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 Unmasked sequence GeneMark 12 genes FGENESH 10 genes 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 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

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: http://bp.nuap.nagoya-u.ac.jp

 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

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

Starch branching enzyme I from rice .

     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.

Image from: http://pdb.rcsb.org

 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 LOC100193963 (si486073c04), mRNA” (E=0.00) (not cDNA)  Other good match was to “ XM_002455881.1

Sorghum bicolor protein, mRNA” (94%, E=0.0

)

hypothetical

 ◦ ◦

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