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expression data publicly available to researchers world-wide...
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Barley1 22k Microarray Sequence ID: Barley1_00048 |
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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_00048:
Expression details for Contig48_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig48_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_Os05g41640.3, phosphoglycerate kinase protein, putative, expressed, Expect:0, match=369/440. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• Brachypodium distachyon Alignment at Brachybase: Bradi2g21120.2, , Expect:0, match=387/440. 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: 01/29/03 P12782 e-125 Phosphoglycerate kinase, chloroplast precursor pir||TVWTGC phosphoglycerate kinase (EC 2.7.2.3) precursor, chloroplast - wheat
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Annotation via Blast
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• BLASTX UniProt: UniRef90_P12782, Phosphoglycerate kinase, chloroplastic n=14 Tax=Pooideae RepID=PGKH_WHEAT, Expect:0, match=395/438. Blast executed on 2012-01-23 against Uniref90 (Release: 2011_12, 14-Dec-2011) show top hits
• BLASTN TIGR Plant Transcript Assemblies: TA30185_4513, Phosphoglycerate kinase, chloroplast precursor [Triticum aestivum (Wheat)], Expect:0, match=1433/1433. Blast executed on 2007-10-23 against TIGR TA Hordeum vulgare release 2 show top hits
• BLASTX NCBI Reference Sequence: NP_001147628, phosphoglycerate kinase [Zea mays], Expect:0, match=364/438. Blast executed on 2010-12-10 against NCBI RefSeq rel-44 show top hits
• BLASTX MSU Rice genome: LOC_Os05g41640.3, phosphoglycerate kinase protein, putative, expressed, Expect:0, match=369/440. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• BLASTN DFCI Hordeum vulgare Gene Index: TC195236, homologue to UniRef100_P12782 Cluster: Phosphoglycerate kinase, chloroplast precursor; n=24; Triticeae|Rep: Phosphoglycerate kinase, chloroplast precursor - Triticum aestivum (Wheat), partial (74%), Expect:0, match=1208/1192. Blast executed on 2010-11-03 against HvGI(DFCI) release 11 show top hits
• BLASTX Brachypodium distachyon genome: Bradi2g21120.2, , Expect:0, match=387/440. 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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AT3G12780.1:| Symbols: PGK1 | phosphoglycerate kinase 1 | chr3:4061127-4063140 REVERSE LENGTH=482
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0 |
354/435
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81.4
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view
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AT1G56190.1:| Symbols: | Phosphoglycerate kinase family protein | chr1:21028403-21030454 FORWARD LENGTH=479
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0 |
352/400
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88
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view
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AT1G56190.2:| Symbols: | Phosphoglycerate kinase family protein | chr1:21028622-21030454 FORWARD LENGTH=406
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0 |
351/399
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88
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view
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AT1G79550.2:| Symbols: PGK | phosphoglycerate kinase | chr1:29924347-29926295 REVERSE LENGTH=402
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0 |
324/397
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81.6
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view
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AT1G79550.1:| Symbols: PGK | phosphoglycerate kinase | chr1:29924347-29926295 REVERSE LENGTH=402
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0 |
324/397
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81.6
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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: 1771
>Barley1_00048
CTCCTCCTCACCACCACCACCCCACCCTCCTCCTCCTCCTCCCCTGATCCCGCTCCCAAT
GGCGTCCACCGCCGCGCAGCCCGCCGCCCTCGTCGCCCGCCGCGTCGCGTCCGCGGCCGC
GCCGCTGCGGCGCGCGGGGCTCGCGGCCGGGTGCCAGCCGGCGCGCTCGCTGGCGTTCGC
GGCCGGCGCCGACCCGCGCCTCGCGGTCCACGTCGCGTCACGCTGCCGGGCCGCCTCGGC
CGCGCGCGGGGCCCGCGCCGTCGCCACCATGGCCAAGAAGAGCGTCGGCGACCTCACCGC
CGCCGACCTCGAGGGCAAGCGCGTGCTCGTGCGGGCCGACCTCAACGTGCCGCTCGACGA
CAACCAGAACATCACCGACGACACCCGCATCCGCGCCGCCATCCCCACCATCAAGTACCT
CCTCACCAACGGCGCCAAGGTCATCCTCACCAGCCACTTGGGTCGTCCTAAGGGTGTTAC
TCCTAAGTTTAGCTTGGCTCCCCTTGTGCCCAGATTGTCCGAGCTTCTTGGTATTGAGGT
GAAAAAAGCAGATGATGTTATTGGCCCAGAAGTTGAAAAGTTGGTGGCTGACCTGGCAAA
TGGTGCTGTTTTGCTCCTCGAAAATGTAAGATTTTACAAGGAAGAGGAGAAGAACGATCC
AGAGTTTGCAAAGAAGCTTGCTTCGCTGGCAGATCTGTTTGTAAACGATGCATTCGGAAC
AGCCCACAGAGCGCATGCGTCGACTGAGGGAGTTACCAAGTTCTTGAAGCCTTCTGTTGC
GGGATTCCTTTTGCAGAAGGAACTTGACTACCTTGATGGAGCTGTTTCAAACCCTAAGCG
CCCATTTGCTGCCATTGTGGGTGGCTCAAAGGTGTCATCCAAGATTGGGGTTATTGAATC
CCTGTTGGAGAAGTGTGATATCCTTCTTTTGGGTGGTGGTATGATCTTCACATTTTACAA
GGCACAAGGACTATCAGTTGGTTCTTCCTTGGTTGAGGAAGATAAACTTGAGTTGGCAAC
ATCTCTGCTTGCAAAAGCAAAGGCAAAGGGTGTCTCCCTTTTGTTGCCATCTGATGTTGT
CATTGCTGATAAGTTTGCTCCTGATGCTAACAGCCAGACCGTGGCAGCATCTGCAATTCC
TGATGGTTGGATGGGGCTGGACATTGGCCCAGATTCAGTCAAAACATTTAATGATGCCCT
GGACACAACACAGACAATCATTTGGAATGGACCAATGGGTGTCTTTGAATTTGACAAGTT
TGCAGTAGGAACGGAGGCTGTTGCAAAGAAGTTGGCCGAGCTTAGCAAAAAGGGTGTGAC
AACTATTATTGGAGGCGGAGACTCCGTCGCGGCTGTCGAGAAGGTGGGAGTGGCTGATGT
TATGAGCCACATCTCAACTGGTGGTGGCGCTAGCTTGGAGTTGTTGGAAGGAAAGCAGCT
TCCTGGAGTCGTTGCACTTGATGAAGGTGTCGTGACGAGCTCGGTGGCCGTATGAGGCTA
AGCTTCATTTTGTTGCATCTTAATTCCTTTCATGTACGGTTCCAAACCTGCCATGTTCTC
CTCCCTCCTTTGCTCTTCAACCACTCGAAATGTAAGGGACCAATGTTTTATAGAGAAATG
CTGGGAACTGTTTGAATAATAACCCCCCAACAATTTGTGCCCAAAAAAAAAAAAAAAAAT
CAGCTCACATAATTAGCACCAGCAAATGTTTTATTTAAAAGGCAAAGATGGAACGAATGT
TTGTTTGCTCCCTCAAAAAAAAAAAAAAAAA
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