Bikash Shakya
Emma Lang
Jorge Diaz
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BLASTx
entire
sequence
against
genomes.
RepeatMasker
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55.47% repetitive sequences
82.5%
retroelements
13.0%
DNA transposons
EMBOSS explorer
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74 CpG islands
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54 inverted repeats
9
plant
GENE PREDICTION
Masked
sequence
Unmasked
sequence
GeneMark
GeneMark
12 genes
27 genes
FGENESH
FGENESH
10 genes
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
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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-transmembranedomain protein 1”
(LOC100284352) mRNA (cDNA)
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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
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conserved domain: MtN3_slv
Sugar efflux transporter
Involved in seed and pollen development
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Starch branching enzyme I from rice.
1 exon
899 amino acids
Soluble protein
1,4-alpha-glucanbranching 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)
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EST data covered almost all of gene III (1 gap)
(intron?)
◦ All EST sequences used had 99%-100% identity with gene III
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Segment without EST data aligns to starch
branching enzyme III in A. thaliana – not an intron
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conserved domains for 1,4-alpha-glucanbranching 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.
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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_002455881.1Sorghum bicolor hypothetical
protein, mRNA” (94%, E=0.0)
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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)
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EST data also have two gaps.
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Conserved domains:
◦ NCBI BlastX
◦ InterProScan