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microarray data publicly available to researchers world-wide...
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Rice 57k Microarray Sequence ID: Os.10220.1.S1_at |
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Sequence Type
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Consensus sequence
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Probe Set Details
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Probe Sequences & Alignment
EXPRESSION DETAILS for Os.10220.1.S1_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Os.10220.1.S1_at
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Alignments and Assemblies
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• PlantGDB PUT assemblies
• PLEXdb Blast
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Model Genome Alignments
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• Rice Alignment at Gramene (by probe set id)
On the Gramene Featureview page, click the probeset location on the chromosome to see the contig view.
• Rice Alignment at Gramene (by locus name): LOC_Os07g48820.2, transcription factor, putative, expressed, Expect:1e-139, match=334/262. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
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Probe Set Annotation
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Affymetrix annotation, 2009-03-11
gb:AB051295.1 /DB_XREF=gi:17025919 /GEN=OsNIF2 /TID=Os.10220.1 /CNT=28 /FEA=FLmRNA /TIER=FL /STK=3 /UG=Os.10220 /DEF=Oryza sativa OsNIF2 mRNA for bZIP transcription factor, complete cds. /PROD=bZIP transcription factor /FL=gb:AB051295.1 gb:AK100440.1 /REP_ORG=O. sativa
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Annotation via Blast
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• BLASTX UniProt: UniRef90_Q7X993, Os07g0687700 protein n=10 Tax=Poaceae RepID=Q7X993_ORYSJ, Expect:1e-139, match=334/262. Blast executed on 2009-07-02 against Uniref90 (July '09) show top hits
• BLASTN TIGR Plant Transcript Assemblies: TA41051_4530, BZIP transcription factor [Oryza sativa (Rice)], Expect:0, match=2206/2207. Blast executed on 2007-10-23 against Oryza sativa release 2 show top hits
• BLASTX Rice genome: LOC_Os07g48820.2, transcription factor, putative, expressed, Expect:1e-139, match=334/262. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• BLASTX NCBI Reference Sequence: NP_001060695, Os07g0687700 [Oryza sativa (japonica cultivar-group)], Expect:1e-139, match=334/262. Blast executed on 2009-09-23 against NCBI RefSeq rel-35 show top hits
• BLASTN DFCI Rice Gene Index: TC295942, UP|Q8W5R9_ORYSA (Q8W5R9) BZIP transcription factor, complete, Expect:0, match=2173/2149. Blast executed on 2009-09-13 against OsGI(DFCI) release 17 show top hits
• BLASTX Arabidopsis thaliana genome: AT5G06950.4, | Symbols: AHBP-1B, TGA2 | AHBP-1B; DNA binding / transcription activator/ transcription factor/ transcription repressor | chr5:2152323-2154174 FORWARD, Expect:1e-102, match=330/197. Blast executed on 2009-09-01 against Arabidopsis thaliana genome, TAIR release 9 show top hits
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Sequence
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Total length: 2207
>Os.10220.1.S1_at gb|AB051295.1
ctctctccacctcctccactctcccaccacnacgagaccttctcgangcttcctcccccc
caaaccccttccgctcctcctcctcctcccaaatccaccacggcgacgccgccgccgcag
agcccctagctcccggaggtccctcgcccccgccagctccgacggcctcacggaaggagg
agtaacgtgggcgttgattggatttttttgttttccccccaccttgagtgagtctgtgcc
gtttccccggcggcgagggagggcagagggctgatcatggtcgtgcgccgccggtgcctt
gccgagatttcccccaaccgccaccgacgatcgttcacttggcacaaaggggagtagcac
tgtccaagctgttgtggtccgtcagggagattggccaacctgtggggtttcagatcgaca
taagtacgtcagtatttcagccatcgatcaatctggcggttcatagggctgtgcttgcaa
cctttctggcagaaaggagagagcaaagtgatttgctgtctcctgttgattgtggcctgt
tgaggcccagtaatggcagatgctagttcaaggactgacacatcgattgttgtagacaac
gacgacaaaaaccaccagttagaaaacggacatagtggtgcagtcatggcttctaactct
tcagatagatctgacagatctgacaaacttatggaccaaaagacaattcggcggcttgct
caaaatcgtgaggcagcaagaaaaagtcggctgaggaaaaaggcatatgtgcaacaacta
gagagcagtaagctgaagcttgcacagctagagcaggaacttcagaaagctcgtcagcag
ggaatcttcatctctagctctggagaccagacccatgccatgagtggaaatggggcattg
acttttgacttagaatacactagatggctcgaggagcaaaataagcagataaatgagttg
aggacagcagtgaatgctcatgcaagtgacagtgaccttcgtcttattgttgatggcata
atggcgcattatgacgaggtattcaaggttaagggtgtagctgcaaaggccgatgtgttt
catatactttcaggcatgtggaagacacccgcagaaagatgcttcctgtggcttggtggt
ttccgtccatctgagcttctaaagctcctagcaaatcacctcgaacctttaaccgagcag
cagttgctgggattaaacaacctccaggaatcttctcagcaggcggaggatgcactttca
caaggtatggaagcactgcagcaatctctggcagatactttggctggatctctcgnttca
tcagggtcttctgggaatgtggcgaactacatgggtcagatggcaatggccatgggtaaa
ctaggaacgctcgagaatttcctttgccaggcggacaacctgcgacagcagacattgcat
caaatgcaacgaattctgacgatccggcaagcctcgcgtgctcttcttgccatacacgat
tacttttcacgcttgcgtgctttgagttcgctgtggcttgctaggccacgggagtaacaa
aatggtcatgtgtgcctgtgacgaggttagacgctcattttgatggacngcagataattg
ggtttttccctgtacaattgtgtttggcagctgtggagctaaagttaaaaactgtaccta
aagtggtgtatgcaaataggtgaagcctctaagtaagttataacgattgcattattgtgt
tagcaataaaagttgggtaattcaggatgtgtcctgagttgttttgttgtagtagaagaa
ctgcatgtagtggctggaaatgcagtgttgaatgtaactaaagctctgctgctcacgttg
cataatgttgtgtagtaatagttagctagtgatgcccattttacctgcactcctctggga
agctgaaactgcaacctgaagcaaccacggtgcagaagaccgcatgcatggtaaatgatt
aaaaggatatatatgggctcaacatcgctgccaaatcctgagataatgaacaggcatgct
aaactgctacttccacatgaaacntcccagttgacatgaagaatgagctgttcagtttta
tggtttctgtgttgcactgtacataattcctgtacgggtctgaanttatcctgaaatcat
gctaaactgcagaagcatatgaaatctccagaccggntgacatgaaa
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