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Barley1 22k Microarray Sequence ID: Barley1_00028 |
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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_00028:
Expression details for Contig28_s_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig28_s_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_Os05g02300.1, Core histone H2A/H2B/H3/H4 domain containing protein, putative, expressed, Expect:1e-35, match=74/102. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• Brachypodium distachyon Alignment at Brachybase: Bradi1g66370.1, , Expect:9e-35, match=70/103. 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: 10/29/02 BAB44136.1 1e-41 putative histone H2A [Oryza sativa (japonica cultivar-group)]
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Annotation via Blast
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• BLASTX UniProt: UniRef90_Q9M531, Histone H2A n=20 Tax=core eudicotyledons RepID=H2A_EUPES, Expect:8e-35, match=75/102. Blast executed on 2012-01-23 against Uniref90 (Release: 2011_12, 14-Dec-2011) show top hits
• BLASTN TIGR Plant Transcript Assemblies: TA30764_4513, Histone H2A [Hyacinthus orientalis (Common hyacinth)], Expect:0, match=675/675. Blast executed on 2007-10-23 against TIGR TA Hordeum vulgare release 2 show top hits
• BLASTX NCBI Reference Sequence: NP_001183510, hypothetical protein LOC100501984 [Zea mays], Expect:1e-35, match=75/103. Blast executed on 2010-12-10 against NCBI RefSeq rel-44 show top hits
• BLASTX MSU Rice genome: LOC_Os05g02300.1, Core histone H2A/H2B/H3/H4 domain containing protein, putative, expressed, Expect:1e-35, match=74/102. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• BLASTN DFCI Hordeum vulgare Gene Index: TC197500, similar to UniRef100_P40280 Cluster: Histone H2A; n=1; Zea mays|Rep: Histone H2A - Zea mays (Maize), partial (96%), Expect:0, match=676/670. Blast executed on 2010-11-03 against HvGI(DFCI) release 11 show top hits
• BLASTX Brachypodium distachyon genome: Bradi1g66370.1, , Expect:9e-35, match=70/103. 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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AT5G59870.1:| Symbols: HTA6 | histone H2A 6 | chr5:24115605-24116144 REVERSE LENGTH=151
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2e-34 |
73/103
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70.9
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view
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AT5G02560.1:| Symbols: HTA12 | histone H2A 12 | chr5:575437-576456 FORWARD LENGTH=154
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1e-33 |
68/102
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66.7
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view
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AT5G27670.1:| Symbols: HTA7 | histone H2A 7 | chr5:9792807-9793365 REVERSE LENGTH=151
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1e-32 |
70/103
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68
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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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4e-29 |
63/103
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61.2
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view
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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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6e-29 |
63/103
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61.2
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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: 692
>Barley1_00028
CGGCAATCAGCAGTCAAGCAATCTCCACACACATCTCTCCTACTCCCGAATCCGTTCTCC
ACCTAGCCATGGACGCCTCAGCCACCGTAGCCGCCGGGAAGGGGAAGAAGGGCGCGGCCG
GGCGCAAGGCCGGCGGCCCCAGGAAGAAGTCCGTGTCGCGGTCCGTCAAGGCCGGGCTCC
AGTTCCCCGTCAGCCGCATCGGGCGCTTCCTCAAGAAGGGCCGCTACGCGCAGCGCGTCG
GTTCCGGCGCCCCCGTCTACCTCGCGGCGGTCCTCGAGTACCTCGCCGCCGAGCTGCTGG
AGCTGGCGGGCAACGCCGCCAAGGACAACAAGAAGAGCCGCATCACCCCCCGCCACCTGC
TGCTCGCCATCAGGAACGACGAGGAGCTCGGCAAGCTGCTCACCGGCATCACCATCGCGC
ACGGCGGCGTCATCCCCAACATCAACCCGGTGCTGCTCCCCAAGAAAACCGCCGAGAAGT
CGCCCAAGGAGCCCAAGTCGCCCAAGAAGACCGCCAAGTCCCCCAAGAAGGCGTAGGCGG
CCATTGCGTAGTTAGGTCGGAGTAGCTGGGATGGATGTTACATGCATGGGTGTGCTTCAG
CTCGAAGCACACTGTTTCCAGTTGTGTCGTTGTATCTTCAGACCTGTGAATTCTATGGAA
CAATGAGTTGCTTTGAAAAAAAAAAAAAAAAA
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