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expression data publicly available to researchers world-wide...
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Barley1 22k Microarray Sequence ID: Barley1_00079 |
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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_00079:
Expression details for Contig79_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig79_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):
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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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LOC_Os06g07220.1:LTPL128 - Protease inhibitor/seed storage/LTP family protein precursor, expressed
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6e-41 |
77/90
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85.6
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view
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LOC_Os06g43600.2:LTPL129 - Protease inhibitor/seed storage/LTP family protein precursor, expressed
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2e-28 |
52/82
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63.4
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view
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LOC_Os06g43600.1:LTPL129 - Protease inhibitor/seed storage/LTP family protein precursor, expressed
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2e-28 |
52/82
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63.4
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view
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LOC_Os04g52260.1:LTPL124 - Protease inhibitor/seed storage/LTP family protein precursor, expressed
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3e-26 |
51/85
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60
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view
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LOC_Os04g52250.1:LTPL123 - Protease inhibitor/seed storage/LTP family protein precursor, expressed
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2e-25 |
51/85
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60
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view
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show best hit only
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• Brachypodium distachyon Alignment at Brachybase: Bradi1g48160.1, , Expect:8e-42, match=79/88. 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 JQ1663 7e-41 hybrid proline-rich protein - maize emb|CAA42959.1| prolin rich protein [Zea mays]
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Annotation via Blast
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• BLASTX UniProt: UniRef90_Q00451, 36.4 kDa proline-rich protein n=2 Tax=Solanum RepID=PRF1_SOLLC, Expect:1e-27, match=57/86. Blast executed on 2012-01-23 against Uniref90 (Release: 2011_12, 14-Dec-2011) show top hits
• BLASTN TIGR Plant Transcript Assemblies: TA28886_4513, Cold acclimation protein WCOR518 [Triticum aestivum (Wheat)], Expect:0, match=527/527. Blast executed on 2007-10-23 against TIGR TA Hordeum vulgare release 2 show top hits
• BLASTX NCBI Reference Sequence: XP_002437917, hypothetical protein SORBIDRAFT_10g004790 [Sorghum bicolor], Expect:4e-41, match=76/89. Blast executed on 2010-12-10 against NCBI RefSeq rel-44 show top hits
• BLASTX MSU Rice 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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LOC_Os06g07220.1:LTPL128 - Protease inhibitor/seed storage/LTP family protein precursor, expressed
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6e-41 |
77/90
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85.6
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view
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LOC_Os06g43600.2:LTPL129 - Protease inhibitor/seed storage/LTP family protein precursor, expressed
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2e-28 |
52/82
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63.4
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view
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LOC_Os06g43600.1:LTPL129 - Protease inhibitor/seed storage/LTP family protein precursor, expressed
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2e-28 |
52/82
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63.4
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view
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LOC_Os04g52260.1:LTPL124 - Protease inhibitor/seed storage/LTP family protein precursor, expressed
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3e-26 |
51/85
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60
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view
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LOC_Os04g52250.1:LTPL123 - Protease inhibitor/seed storage/LTP family protein precursor, expressed
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2e-25 |
51/85
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60
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view
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show best hit only
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• BLASTN DFCI Hordeum vulgare Gene Index: TC209532, similar to UniRef100_Q41848 Cluster: Prolin rich protein; n=3; Zea mays|Rep: Prolin rich protein - Zea mays (Maize), partial (57%), Expect:0, match=1193/731. Blast executed on 2010-11-03 against HvGI(DFCI) release 11 show top hits
• BLASTX Brachypodium distachyon genome: Bradi1g48160.1, , Expect:8e-42, match=79/88. Blast executed on 2010-11-03 against Brachypodium distachyon genome, Brachybase release 1 show top hits
• BLASTX Arabidopsis thaliana genome: AT3G22142.1, | Symbols: | Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein | chr3:7803604-7808046 REVERSE LENGTH=1481, Expect:2e-31, match=55/85. 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: 999
>Barley1_00079
GACACCACCACCCGCCCCACCACGGCAAGCCGCCCAAGCACCACCCCGGCCCGCCGTCGG
GGCCCAAATGCCCGCCGTGCCACCCGCCTCCCACGCCGCGCCCACCGCCGACTCCGCCGT
ACGGGCCTCCCACGCCACTGCCACCGCCTTACGTGCCGCCCACGCCGCCCTACACCCCGC
CGTCGCCACCGTACATTCCGCCAAGCCCGCCGTACGTGCCACCAACGCCACTGCCTCCGC
CGTACGTGCCACCATACGTCCCACCGACACCTCCATACACTCCTCCCTACGTGCCGCCAA
CCCCGCCATACGTCCCGCCGTCGCCGCCCTACGTGCCACCGACACCGCCATACACGCCGC
CGTACGTGCCGCCGCCGTCGCCGGGGAGGAAGACGTGCCCGATCGACGCGCTGAAGCTGA
ACGCGTGCGTGGACGTGCTGAGCGGACTGGTGCACCTGGTGATCGGGCGGGAGGCGCGGA
GCAAGTGCTGCCCGCTGGTGCAGGGGGTGGCGGACCTGGACGCGGCGCTGTGCCTCTGCA
CCACCATCCGGGCGCGGGTCCTCAACATCAACATCTACCTCCCGGTGGCGCTCCGGCTGC
TCATCACCTGCGGCAAGCACCCGCCCAACGGCTTCCAGTGCCCCACCGTCCTCGACGCCT
AGCCTAGCCTAGCCTGCATGGCCGCTCTGGCTCGGCTCTCGCCATAGCTTTACTACCATA
CTAGCGTGTGGCGTGGGGTGCTACAGTGCTTGCTCGCTCCAGTGCTGTGCGTGCCTGCGA
TTTGTGTGCGTCTCGATCGACCTCGACCGATTTTCTTGTTCCGTGTTAGTAGTGTGTAGG
AGTGTGGCAACTCCATGTGGTTTCCGGCCAAGTGATGTTGAATAATTAATTAATTAACAT
GTGCTATTTAAGTACAAAAAAAAAAAAAAAGTCCGTGTATTGTAACGGAAGAAAAAAAAT
TTATAATTTTCAATTGTGATAAAAAAAAAAAAAAAAAAA
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