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expression data publicly available to researchers world-wide...
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Barley1 22k Microarray Sequence ID: Barley1_00076 |
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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_00076:
Expression details for Contig76_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig76_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:2e-39, match=80/106. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• Brachypodium distachyon Alignment at Brachybase: Bradi1g66370.1, , Expect:6e-41, match=82/107. 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: 11/06/02 P19177 5e-43 Histone H2A pir||S11498 histone H2A - parsley
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Annotation via Blast
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• BLASTX UniProt:
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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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UniRef90_P19177:Histone H2A n=3 Tax=Magnoliophyta RepID=H2A_PETCR
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5e-39 |
83/107
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77.6
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view
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UniRef90_Q1S053:Probable histone H2A.3 n=3 Tax=Medicago truncatula RepID=H2A3_MEDTR
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7e-39 |
81/107
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75.7
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view
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UniRef90_Q75L11:Probable histone H2A.6 n=5 Tax=Oryza sativa RepID=H2A6_ORYSJ
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5e-38 |
80/106
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75.5
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view
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UniRef90_P40280:Histone H2A n=7 Tax=Poaceae RepID=H2A_MAIZE
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2e-37 |
79/107
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73.8
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view
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UniRef90_P02276:Histone H2A.2.1 n=2 Tax=Triticum aestivum RepID=H2A2_WHEAT
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3e-37 |
77/106
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72.6
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view
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show best hit only
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• BLASTN TIGR Plant Transcript Assemblies: TA30079_4513, Histone H2A [Hyacinthus orientalis (Common hyacinth)], Expect:0, match=664/664. 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:9e-40, match=82/107. 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:2e-39, match=80/106. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• BLASTN DFCI Hordeum vulgare Gene Index: TC198429, similar to UniRef100_P40280 Cluster: Histone H2A; n=1; Zea mays|Rep: Histone H2A - Zea mays (Maize), partial (91%), Expect:0, match=670/659. Blast executed on 2010-11-03 against HvGI(DFCI) release 11 show top hits
• BLASTX Brachypodium distachyon genome: Bradi1g66370.1, , Expect:6e-41, match=82/107. Blast executed on 2010-11-03 against Brachypodium distachyon genome, Brachybase release 1 show top hits
• BLASTX Arabidopsis thaliana genome: AT5G02560.1, | Symbols: HTA12 | histone H2A 12 | chr5:575437-576456 FORWARD LENGTH=154, Expect:7e-37, match=74/106. 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: 681
>Barley1_00076
CCGCAATCCACCAACCACCATCACCAAATCTCTCTGCCCCTATCCAGCTTTCTCTCAAAA
GCTCCGTCTGTCAGCAATGGAGGTTTCAGGCGCTGCAGCGAAGGGAAAGAAGGGCGCTGC
AGGGCGCAAGGCCGGCGGCCCGAGGAAGAAGTCAGTGACGCGGTCCGTGAAGGCCGGGCT
CCAGTTCCCCGTCGGCCGCATCGGGCGCTACCTCAAGAAGGGCCGGTACGCGCAGCGCGT
CGGCACCGGTGCCCCCGTCTACCTCGCCGCCGTCCTCGAGTACCTGGCTGCCGAGCTGCT
GGAGCTCGCCGGGAACGCCGCCAAGGACAACAAGAAGAGCCGCATCATCCCGCGCCACCT
GCTGCTCGCCGTCAGGAACGACGAGGAGCTCGGAAAGCTGCTGGCCGGCGTCACCATCGC
GCACGGCGGCGTGATCCCCAAGATCAACCCGGTGCTGCTCCCCAAGAGGACCGCGGAGAA
GGAGGGCAAGGGGCCCAAGTCCCCCAAGAAGGCCACCAAGTCCCCGAAGAAGGCCACCAA
GGCTTAGGAACACGCATAGGTTGATGTAGGTTGCTTAATGTCTGTAACATTGGTCGTTGT
TTGGCTAATGGTGTCGATGTAATCTTTGCTGTTAAGAGTAATGTCAGAAATCACTCTGAT
CCGGAAAAAAAAAAAAAAAAA
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