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microarray data publicly available to researchers world-wide...
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Grape Vitis vinifera 16k Microarray Sequence ID: 1607001_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 1607001_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for 1607001_at
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Alignments and Assemblies
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• PlantGDB PUT assemblies
• PLEXdb Blast
• TAIR Blast
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Model Genome Alignments
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• Grape Genome Browser (Gramene): GSVIVG00014415001, pep:novel chromosome:8X:18:12194290:12198185:-1 gene: transcript:GSVIVT00014415001, Expect:0, match=448/417. Blast executed on 2009-01-08 against Vitis Vinifera 8X assembly, Dec 2007 show top hits
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Probe Set Annotation
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Affymetrix annotation, 2009-03-11
gb:CF404264 /DB_XREF=gi:34362679 /DB_XREF=CSECS024B06_PREu0032 /CLONE=CSECS024B06 /TID=Vvi.304.1 /CNT=30 /FEA=EST /TIER=Stack /STK=6 /UG=Vvi.304 /UG_TITLE=Vitis vinifera transcribed sequence with strong similarity to protein sp:P12411 (A.thaliana) TBB1_ARATH Tubulin beta-1 chain /REP_ORG=V. vinifera
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Annotation via Blast
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• BLASTX UniProt: UniRef90_B9FIN1, Putative uncharacterized protein n=2 Tax=Oryza sativa RepID=B9FIN1_ORYSJ, Expect:0, match=624/397. Blast executed on 2009-07-02 against Uniref90 (July '09) show top hits
• BLASTN TIGR Plant Transcript Assemblies: TA37285_29760, Tubulin beta-6 chain [Gossypium hirsutum (Upland cotton)], Expect:0, match=1615/1615. Blast executed on 2007-10-23 against TIGR TA Vitis vinifera release 5 show top hits
• BLASTX NCBI Reference Sequence: XP_002275306, PREDICTED: hypothetical protein [Vitis vinifera], Expect:0, match=448/417. Blast executed on 2009-09-23 against NCBI RefSeq rel-35 show top hits
• BLASTN DFCI Vitis vinifera Gene Index: TC77029, UniRef100_A7NSU9 Cluster: Chromosome chr18 scaffold_1, whole genome shotgun sequence; n=1; Vitis vinifera|Rep: Chromosome chr18 scaffold_1, whole genome shotgun sequence - Vitis vinifera (Grape), partial (83%), Expect:0, match=1430/1212. Blast executed on 2009-09-13 BLAST executed 9/15/09 against VvGI(DFCI) release 6 show top hits
• BLASTX Arabidopsis thaliana genome: AT1G75780.1, | Symbols: TUB1 | TUB1; GTP binding / GTPase/ structural molecule | chr1:28451378-28453602 REVERSE, Expect:0, match=447/407. Blast executed on 2009-09-01 against Arabidopsis thaliana genome, TAIR release 9 show top hits
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Additional Annotations
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From Grant Cramer, University of Nevada, Reno, NV
| UniProt: |
(Q6VAF6) Tubulin beta-6 chain (Beta-6 tubulin) |
| MIPS: |
42.04.05 microtubule cytoskeleton |
| Annotation: |
homologue to UP|TBB1_ARATH (P12411) Tubulin beta-1 chain (Beta-1 tubulin), complete |
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Sequence
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Total length: 1681
>1607001_at gb|CF404264; /DB_XREF=CSECS024B06_PREu0032 /CLONE=CSECS024B06
cccgcgaactcctccnnaaccaccatcaccaccaccactcaatttttggttttcgttttc
attttcattctcnccaaacacaaaaacgatgagggagatcttgcacgttcagggaggcca
atgcggtaaccaaattggatccaagttctgggaggtcatctgcgacgagcacggtgtgga
tcccactgggaggtacaacggagatggttcatctgatcttcagttggagaggatcaatgt
ctactacaatgaggcttctggtggaaggtacgttcccagggctgttctcanggatcttga
gcctgggactatggacagtatcagatcgggaccgtatgggcagatctttcgccctgataa
tttcgtttttggtcagtccggtgccggcaacaattgggccaagggtcattatactgaggg
ggcggagttgattgatgcggttctcgatgttgttcgcaaggaggctgagaattgtgattg
catgcaaggttttcaagtgtgccactcacttggaggaggcactggttctggcatggggac
cctcctgatatcaaagatgagagaggaatacccagatagaatgatgctcactttctccgt
cttcccatctncnaaggtctctgacacagttgtggagccatataatgccaccctctcggt
gcaccagttggtngngaatgctgacgaatgcatggttctggacaatgaggctctttatga
tatttgtttcaggactctcaagctcagcactcctagctttggtgacctgaaccacttgat
ctctgcgacnatgagtggggtgacttgctgcctgaggttccctggccagctgaactcaga
cctccgcaagctggctgtgaatctgatcccgttccctcgccttcatttctttatggtggg
ttttgcaccactcacctctcgtggatcccagcagtacatctccctcacagtgccagagct
aactcagcaaatgtgggatgccaagaacatgatgtgtgcggctgaccctcggcatggccg
ctacctgactgcctcggccatgttcaggggaaagatgagcaccaaggaggtggacgaaca
gatgatcaatgtgcaaaacaaaaactcgtcatattttgtggagtggattcctaataacgt
gaaatctagtgtgtgcgatattccaccaagaggtctgaagatggcatctacatttgtggg
gaactccacttcaatccaggagatgttcaggagggtgagcgagcagttcacagccatgtt
caggcgcaaggctttcttgcactggtatactggggaaggaatggatgagatggaattcac
ggaagcagagagcaacatgaatgatttggtgtcagaataccagcaataccaggatgcaac
tgctgatgacgagggtgagtatgaggagggcccagaagagaattatgaggcctaaaagcc
ttaaagcctaaataagattttgggagatgagcacctaagctttgcccatttatctgctac
tactatatgtggctgttanagtttcagatttatttccattttgcttgcagcttgtttgta
tcgtcacctggtttgaatcttctcttccataatataatgtttgtgggttgtgttcnannn
aaaaaaaaaaaaaannannnnnnaaannnnnnaaaaaaaaaaaaaaaaaaaaannnnnaa
a
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