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Barley1 22k Microarray Sequence ID: Barley1_00074
Sequence ID: You may enter either an Affymetrix probe set ID or a Barley1 consensus ID
Sequence Type Exemplar sequence
Probe Set Details Probe Sequences & Alignment
Probe sets for Barley1_00074:

Expression details for Contig74_x_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig74_x_at
Alignments and Assemblies • 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
Model Genome Alignments • Rice Alignment at Gramene (by locus name): LOC_Os09g17740.1, chlorophyll A-B binding protein, putative, expressed, Expect:2e-16, match=37/38. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits

• 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
Probe Set Annotation 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
Annotation via Blast • BLASTX UniProt:
Subject Sequence Description   Expect   Identity/Match   Identity%   HSP
Details
UniRef90_P14584:Chlorophyll a-b binding of LHCII type 1 protein (Fragment) n=20 Tax=Magnoliophyta RepID=CB21_RAPSA 3e-15 38/38 100 view
UniRef90_P14276:Chlorophyll a-b binding protein 3A, chloroplastic (Fragments) n=4 Tax=Solanum lycopersicum RepID=CB2E_SOLLC 4e-15 37/38 97.4 view
UniRef90_P0CJ48:Chlorophyll a-b binding protein 2, chloroplastic n=19 Tax=Magnoliophyta RepID=CB1A_ARATH 4e-15 37/38 97.4 view
UniRef90_P08222:Chlorophyll a-b binding protein of LHCII type 1 (Fragment) n=7 Tax=Magnoliophyta RepID=CB22_CUCSA 6e-15 37/38 97.4 view
UniRef90_P12330:Chlorophyll a-b binding protein 1, chloroplastic n=26 Tax=Poaceae RepID=CB21_ORYSJ 6e-15 37/38 97.4 view
show best hit only

• 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: LOC_Os09g17740.1, chlorophyll A-B binding protein, putative, expressed, Expect:2e-16, match=37/38. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits

• 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.
Additional Annotations No additional annotations found for this probe set.
Sequence Total length: 330
>Barley1_00074
CTTCGTCCAGGCCATCGTCACCGGCAAGGGCCCCCTCGAGAACCTCGCCGACCACCTCGC
CGACCCCGTCAACAACAACGCCTGGGCCTTCGCCACCAACTTCGTCCCCGGCAAGTGAGC
TCAACCTCTAGCGCGCGCGCGCGCGCGCGCGCTTGGCCGACAACTTCATTGCTGATGGAT
GCTGCTGTGCTGCATGTCTTTCCGGACTGATAGATGTTGCATGTGAGGGCGAGTCGAGAT
GATGAGTTGGTGTGTGTACACTAAAAAGATGGTGTTTGTGTAATATCTGGTTATTTTTCA
GATTAACCAAGGCAAAAAAAAAAAAAAAAA
 
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