bikash shakya emma lang jorge diaz. blastx entire sequence against 9 plant genomes. repeatmasker ...
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Group 6Bikash Shakya
Emma LangJorge 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
Sequence 6
GENE PREDICTION
Masked sequence
GeneMark
12 genes
FGENESH10 genes
Unmaskedsequence
GeneMark
27 genes
FGENESH28 genes
BLASTx7 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 exonsRNA Evidence BLAST search in the refseq_rna database Zea mays uncharacterized LOC100194332
(LOC100194332), mRNA (cDNA) Identity:100% E-value:0Sequence alignment with the translated sequences
Final Gene Model PredictionFour genes: I, II, III, IV
GENE IPerfect match
EST Evidence
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
Gene II
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
Gene II RNA and EST Evidence
conserved domain: MtN3_slv
Sugar efflux transporter Involved in seed and pollen development
GENE II Protein Function
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.
Gene III
Starch branching enzyme I from rice.
Image from: http://pdb.rcsb.org
99% match to “Zea mays starch branching enzyme III (sbe3)” mRNA (not cDNA)
Gene III RNA and EST Evidence
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.
GENE III Protein Function
5 exons 583 amino acids Membrane protein with 10 trans-membrane helices Amino acid transporter Matched orthologs in wheat and sorghum genomes.
Gene IV
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)
Gene IV: RNA Evidence
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.
Gene IV: EST Evidence
Gene IV: BlastX in Nov. 2012
Conserved domains: ◦ NCBI BlastX
◦ InterProScan
GENE IV: Protein Function