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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: 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: 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:
Subject Sequence Description   Expect   Identity/Match   Identity%   HSP
Details
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 ( 1e-86 1063/291 100 view
TC231386:UniRef100_O04685 Cluster: Chlorophyll a/b-binding protein; n=1; Mesembryanthemum crystallinum|Rep: Chlorophyll a/b-binding protein - Mesembryanthemum crystallinum (Common ice plant), partial (24%) 1e-86 565/291 100 view
TC224677:homologue to UniRef100_O04685 Cluster: Chlorophyll a/b-binding protein; n=1; Mesembryanthemum crystallinum|Rep: Chlorophyll a/b-binding protein - Mesembryanthemum crystallinum (Common ice plant), partial (28%) 1e-86 1236/291 100 view
TC220478:UniRef100_A4ZGB5 Cluster: Chloroplast chlorophyll a/b-binding protein; n=1; Agave tequilana|Rep: Chloroplast chlorophyll a/b-binding protein - Agave tequilana, partial (36%) 1e-86 469/291 100 view
TC198489:homologue to UniRef100_P12329 Cluster: Chlorophyll a-b binding protein 1, chloroplast precursor; n=1; Zea mays|Rep: Chlorophyll a-b binding protein 1, chloroplast precursor - Zea mays (Maize), partial (98%) 1e-86 1085/291 100 view
show best hit only

• 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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