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Barley1 22k Microarray Sequence ID: Barley1_00016 |
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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_00016:
Expression details for Contig16_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig16_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): LOC_Os12g34510.1, Core histone H2A/H2B/H3/H4 domain containing protein, putative, expressed, Expect:1e-44, match=94/120. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• Brachypodium distachyon Alignment at Brachybase: Bradi4g06010.1, , Expect:4e-45, match=94/120. 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: 11/04/02 NP_175868.1 9e-47 histone H2A, putative; protein id: At1g54690.1, supported by cDNA: 16879., supported by cDNA: gi_15724171, supported by
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Annotation via Blast
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• BLASTX UniProt: UniRef90_Q2QPG9, Probable histone H2AXb n=8 Tax=Poaceae RepID=H2AXB_ORYSJ, Expect:3e-43, match=94/120. Blast executed on 2012-01-23 against Uniref90 (Release: 2011_12, 14-Dec-2011) show top hits
• BLASTN TIGR Plant Transcript Assemblies: TA30091_4513, Histone H2A [Chlamydomonas reinhardtii], Expect:0, match=653/653. Blast executed on 2007-10-23 against TIGR TA Hordeum vulgare release 2 show top hits
• BLASTX NCBI Reference Sequence: XP_002328535, histone 2 [Populus trichocarpa], Expect:2e-44, match=93/120. Blast executed on 2010-12-10 against NCBI RefSeq rel-44 show top hits
• BLASTX MSU Rice genome: LOC_Os12g34510.1, Core histone H2A/H2B/H3/H4 domain containing protein, putative, expressed, Expect:1e-44, match=94/120. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• BLASTN DFCI Hordeum vulgare Gene Index: TC233287, homologue to UniRef100_A2Q3H4 Cluster: Histone H2A; Histone-fold; n=1; Medicago truncatula|Rep: Histone H2A; Histone-fold - Medicago truncatula (Barrel medic), partial (94%), Expect:0, match=761/703. Blast executed on 2010-11-03 against HvGI(DFCI) release 11 show top hits
• BLASTX Brachypodium distachyon genome: Bradi4g06010.1, , Expect:4e-45, match=94/120. Blast executed on 2010-11-03 against Brachypodium distachyon genome, Brachybase release 1 show top hits
• BLASTX Arabidopsis thaliana 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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AT1G54690.1:| Symbols: HTA3, H2AXB, G-H2AX, GAMMA-H2AX | gamma histone variant H2AX | chr1:20414607-20415206 REVERSE LENGTH=143
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4e-45 |
93/120
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77.5
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view
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AT1G08880.1:| Symbols: HTA5, H2AXA, G-H2AX, GAMMA-H2AX | Histone superfamily protein | chr1:2847144-2847676 REVERSE LENGTH=143
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5e-45 |
93/120
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77.5
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view
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AT4G27230.2:| Symbols: HTA2 | histone H2A 2 | chr4:13637515-13638325 REVERSE LENGTH=132
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2e-37 |
79/109
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72.5
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view
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AT4G27230.1:| Symbols: HTA2 | histone H2A 2 | chr4:13637515-13638325 REVERSE LENGTH=132
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2e-37 |
79/109
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72.5
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view
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AT5G54640.1:| Symbols: HTA1, RAT5, ATHTA1 | Histone superfamily protein | chr5:22196540-22197279 FORWARD LENGTH=131
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3e-37 |
79/109
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72.5
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view
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show best hit only
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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: 735
>Barley1_00016
CAGCAATCTGTCCGACTCCGGCCATCTCTCCGGCAACCACCGTATCCGCGCGTCCACCAT
CCGTAGCGACCAGAAGATGAGTTCTGCCGGCGGCGGGAGGGGCAAGGCCAAGGCGGCGTC
CAAGATCGTCTCGCGGTCTTCCAAGGCCGGCCTCCAGTTCCCCGTCGGCCGCATCGCCAG
GTACCTCAAGATCGGCAAGTACGCCCAGCGCGTCGGTGCCGGCGCCCCCGTCTACCTCTC
CGCCGTCCTCGAGTACCTCGCCGCTGAGGTCCTGGAGCTCGCCGGCAACGCTGCGCGCGA
CAACAAGAAGACCCGGATCGTGCCGCGCCACATCCAGCTGGCGGTCCGCAACGATGAGGA
GCTGAGTCGGCTTCTGGGCACGGTCACCATTGCCGCCGGCGGTGTGCTGCCCAACATCCA
CACGACGCTGCTCCCCAAGAAAGTCGGCAAGGGCAAGGGCGACATCGGCTCTGCGTCGCA
GGAGTTCTAGAGCCTCGCAGATGAAACCAGCATCATCACAGAAGATTTGAGGACTCTTCT
TTTTCTAGTATGGCGATGCTTTAGGTTGTTAGATTAGTTCTCGGTCAATGCTTTGGTTGG
TGTATCGATGATGAATCTGGTTGGAATGGAATGCTAGCAATCTGGTTCTAGTTAAAAAAA
AAAAAAAATGCTCCTTGTGATATGCCAAATCAAAGTGAAAATATCTTGTTAATCTGGGTA
TGAAAAAAAAAAAAA
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