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expression data publicly available to researchers world-wide...
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Barley1 22k Microarray Sequence ID: Barley1_00074 |
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Sequence Type
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Exemplar sequence
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Probe Set Details
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Probe Sequences & Alignment
- Probe sets for Barley1_00074:
Expression details for Contig74_x_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig74_x_at
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Alignments and Assemblies
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• Barley1 GeneChip Assembly
• Barley1 GeneChip Assembly 25 contig and alignment
• PlantGDB PUT assemblies
• GrainGenes Blast
• HarvEST: Barley 21 Assembly
• HarvEST: Barley 25 Assembly
• HarvEST BLAST
• PLEXdb Blast
• TAIR Blast
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Model Genome Alignments
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• Rice Alignment at Gramene (by locus name):
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Subject Sequence Description
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Expect
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Identity/Match
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Identity%
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HSP
Details
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LOC_Os09g17740.1:chlorophyll A-B binding protein, putative, expressed
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2e-16 |
37/38
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97.4
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view
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LOC_Os01g52240.1:chlorophyll A-B binding protein, putative, expressed
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2e-16 |
37/38
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97.4
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view
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LOC_Os01g41710.1:chlorophyll A-B binding protein, putative, expressed
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2e-16 |
37/38
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97.4
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view
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LOC_Os03g39610.2:chlorophyll A-B binding protein, putative, expressed
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3e-14 |
33/38
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86.8
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view
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LOC_Os03g39610.1:chlorophyll A-B binding protein, putative, expressed
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3e-14 |
33/38
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86.8
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view
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show best hit only
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• Brachypodium distachyon Alignment at Brachybase: Bradi3g42620.1, , Expect:3e-17, match=38/38. Blast executed on 2010-11-03 against Brachypodium distachyon genome, Brachybase release 1 show top hits
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| Probe Set Annotation
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Affymetrix annotation, 2009-03-11
BEST BLASTX NR: 11/06/02 A24039 7e-16 chlorophyll a/b-binding protein 1A precursor - tomato (fragments) prf||1204205A protein 1A,chlorophyll binding
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Annotation via Blast
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• BLASTX UniProt: UniRef90_P14584, Chlorophyll a-b binding of LHCII type 1 protein (Fragment) n=20 Tax=Magnoliophyta RepID=CB21_RAPSA, Expect:3e-15, match=38/38. Blast executed on 2012-01-23 against Uniref90 (Release: 2011_12, 14-Dec-2011) show top hits
• BLASTN TIGR Plant Transcript Assemblies: BJ451134, Light harvesting chlorophyll a /b binding protein of PSII [Euglena gracilis], Expect:2e-86, match=161/161. Blast executed on 2007-10-23 against TIGR TA Hordeum vulgare release 2 show top hits
• BLASTX NCBI Reference Sequence: XP_002881334, chlorophyll A-B-binding protein 2 precursor [Arabidopsis lyrata subsp. lyrata], Expect:4e-16, match=38/38. Blast executed on 2010-12-10 against NCBI RefSeq rel-44 show top hits
• BLASTX MSU Rice genome:
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Subject Sequence Description
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Expect
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Identity/Match
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Identity%
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HSP
Details
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LOC_Os09g17740.1:chlorophyll A-B binding protein, putative, expressed
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2e-16 |
37/38
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97.4
|
view
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LOC_Os01g52240.1:chlorophyll A-B binding protein, putative, expressed
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2e-16 |
37/38
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97.4
|
view
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LOC_Os01g41710.1:chlorophyll A-B binding protein, putative, expressed
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2e-16 |
37/38
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97.4
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view
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LOC_Os03g39610.2:chlorophyll A-B binding protein, putative, expressed
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3e-14 |
33/38
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86.8
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view
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LOC_Os03g39610.1:chlorophyll A-B binding protein, putative, expressed
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3e-14 |
33/38
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86.8
|
view
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show best hit only
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• BLASTN DFCI Hordeum vulgare Gene Index: BE422434, homologue to UniRef100_P07370 Cluster: Chlorophyll a-b binding protein 1B, chloroplast precursor; n=1; Solanum lycopersicum|Rep: Chlorophyll a-b binding protein 1B, chloroplast precursor - Solanum lycopersicum (Tomato) (Lycopersicon esculentum), partial (, Expect:1e-86, match=1063/291. Blast executed on 2010-11-03 against HvGI(DFCI) release 11 show top hits
• BLASTX Brachypodium distachyon genome: Bradi3g42620.1, , Expect:3e-17, match=38/38. Blast executed on 2010-11-03 against Brachypodium distachyon genome, Brachybase release 1 show top hits
• BLASTX Arabidopsis thaliana genome: AT2G34420.1, | Symbols: LHB1B2, LHCB1.5 | photosystem II light harvesting complex gene B1B2 | chr2:14522716-14523513 REVERSE LENGTH=266, Expect:4e-17, match=38/38. Blast executed on 2010-12-10 against Arabidopsis thaliana genome, TAIR release 10 show top hits
Barley1 exemplars are kindly provided by Dr. Timothy Close from HarvEST:Barley. The BLASTs in this section are based on contig assembly #25.
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Additional Annotations
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No additional annotations found for this probe set.
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Sequence
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Total length: 330
>Barley1_00074
CTTCGTCCAGGCCATCGTCACCGGCAAGGGCCCCCTCGAGAACCTCGCCGACCACCTCGC
CGACCCCGTCAACAACAACGCCTGGGCCTTCGCCACCAACTTCGTCCCCGGCAAGTGAGC
TCAACCTCTAGCGCGCGCGCGCGCGCGCGCGCTTGGCCGACAACTTCATTGCTGATGGAT
GCTGCTGTGCTGCATGTCTTTCCGGACTGATAGATGTTGCATGTGAGGGCGAGTCGAGAT
GATGAGTTGGTGTGTGTACACTAAAAAGATGGTGTTTGTGTAATATCTGGTTATTTTTCA
GATTAACCAAGGCAAAAAAAAAAAAAAAAA
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