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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: UniRef90_P19177, Histone H2A n=3 Tax=Magnoliophyta RepID=H2A_PETCR, Expect:5e-39, match=83/107. Blast executed on 2012-01-23 against Uniref90 (Release: 2011_12, 14-Dec-2011) show top hits
• 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:
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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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TC198429:similar to UniRef100_P40280 Cluster: Histone H2A; n=1; Zea mays|Rep: Histone H2A - Zea mays (Maize), partial (91%)
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0 |
670/659
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100
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view
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TC198894:similar to UniRef100_P40280 Cluster: Histone H2A; n=1; Zea mays|Rep: Histone H2A - Zea mays (Maize), partial (92%)
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0 |
645/456
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95.8
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view
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TC221843:similar to UniRef100_P40280 Cluster: Histone H2A; n=1; Zea mays|Rep: Histone H2A - Zea mays (Maize), partial (91%)
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0 |
723/451
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94.7
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view
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BG343988:similar to UniRef100_A5AFR3 Cluster: Histone H2A; n=1; Vitis vinifera|Rep: Histone H2A - Vitis vinifera (Grape), partial (94%)
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0 |
718/449
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94.3
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view
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TC236341:homologue to UniRef100_A2WQG7 Cluster: Probable histone H2A.5; n=2; Oryza sativa|Rep: Probable histone H2A.5 - Oryza sativa subsp. indica (Rice), partial (91%)
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0 |
829/414
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93.2
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view
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show best hit only
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• 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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