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Barley1 22k Microarray Sequence ID: Barley1_00085 |
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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_00085:
Expression details for Contig85_x_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig85_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): LOC_Os03g17100.1, Core histone H2A/H2B/H3/H4 domain containing protein, putative, expressed, Expect:4e-40, match=83/114. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• Brachypodium distachyon Alignment at Brachybase: Bradi1g66360.3, , Expect:2e-41, match=87/126. 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: 10/13/02 S53518 7e-46 histone H2A.2 - wheat dbj|BAA07276.1| protein H2A [Triticum aestivum]
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Annotation via Blast
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• BLASTX UniProt: UniRef90_Q43214, Protein H2A.6 n=11 Tax=Triticeae RepID=H2A6_WHEAT, Expect:1e-43, match=93/114. Blast executed on 2012-01-23 against Uniref90 (Release: 2011_12, 14-Dec-2011) show top hits
• BLASTN TIGR Plant Transcript Assemblies: TA30092_4513, Protein H2A [Triticum aestivum (Wheat)], Expect:0, match=696/700. Blast executed on 2007-10-23 against TIGR TA Hordeum vulgare release 2 show top hits
• BLASTX NCBI Reference Sequence:
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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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NP_001183439:hypothetical protein LOC100501869 [Zea mays]
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5e-40 |
85/114
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74.6
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view
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NP_001183510:hypothetical protein LOC100501984 [Zea mays]
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1e-39 |
84/114
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73.7
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view
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NP_001049731:Os03g0279200 [Oryza sativa Japonica Group]
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2e-39 |
83/114
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72.8
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view
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NP_001043136:Os01g0502700 [Oryza sativa Japonica Group]
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2e-39 |
83/114
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72.8
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view
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XP_002463507:hypothetical protein SORBIDRAFT_01g000950 [Sorghum bicolor]
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3e-39 |
83/114
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72.8
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view
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show best hit only
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• BLASTX MSU Rice genome: LOC_Os03g17100.1, Core histone H2A/H2B/H3/H4 domain containing protein, putative, expressed, Expect:4e-40, match=83/114. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• BLASTN DFCI Hordeum vulgare Gene Index: BQ760420, homologue to UniRef100_P02275 Cluster: Histone H2A.1; n=1; Triticum aestivum|Rep: Histone H2A.1 - Triticum aestivum (Wheat), complete, Expect:0, match=695/671. Blast executed on 2010-11-03 against HvGI(DFCI) release 11 show top hits
• BLASTX Brachypodium distachyon genome: Bradi1g66360.3, , Expect:2e-41, match=87/126. Blast executed on 2010-11-03 against Brachypodium distachyon genome, Brachybase release 1 show top hits
• BLASTX Arabidopsis thaliana genome: AT5G27670.1, | Symbols: HTA7 | histone H2A 7 | chr5:9792807-9793365 REVERSE LENGTH=151, Expect:2e-37, match=78/112. 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: 713
>Barley1_00085
TCCGATCCAGCAACACCGCCGCCAACACCACACCTTGAAGGACCTCGACGCCGGAGAAGC
AGCAAGCAAGCAAGATGGCCGGAAGGAAGGGCGGCGACAGGAAGAAGGCGGTGACCAGGT
CCGTGAAGGCCGGGCTCCAGTTCCCCGTCGGCCGCATCGGGCGCTACCTCAAGAAGGGCC
GCTACGCCCAGCGCGTCGGCTCCGGCGCCCCCGTCTACCTCGCCGCCGTCCTCGAGTACC
TCGCCGCAGAGGTCCTGGAGCTCGCCGGCAACGCGGCCAAGGACAACAAGAAGTCCCGCA
TCATCCCGCGCCACCTGCTTCTCGCCGTCCGCAACGACCAGGAGCTCGGCAGGCTGCTCG
CCGGCGTCACCATCGCCCACGGCGGCGTCATCCCCAACATCAACTCCGTGCTGCTCCCCA
AGAAGTCCGCCGCCGCTGCCGAGAAGGAGGCCACCAAGTCGCCCAAGAAGAATACCGCCA
CCAAGTCCCCCAAGAAGAAGGCCGCCGCCAAGGAGTAGCCTAGCTGACACTTAGTTCGTT
ATCAGTGAGAAGATGAGCAGACTTTTGGTTGATTGGATCATGTATGTAAATGCCAGTCTG
TATTGGCTCTTTCATTTGTTCGATGAAGAGGCCAGTCAGGACTGTATTTTACCTGTGATT
TAGTATTTGATCAATGACTGAAGATGCCACACTTTCAATCAAAAAAAAAAAAA
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