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Barley1 22k Microarray Sequence ID: Barley1_00039 |
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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_00039:
Expression details for Contig39_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig39_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_Os04g14760.1, phosphoglycerate mutase, putative, expressed, Expect:4e-98, match=178/236. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• Brachypodium distachyon Alignment at Brachybase: Bradi5g03700.1, , Expect:1e-107, match=197/236. 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 NP_568040.1 6e-60 (NM_119999) expressed protein; protein id: At4g38370.1, supported by cDNA: 249631. [Arabidopsis thaliana]
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Annotation via Blast
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• BLASTX UniProt: UniRef90_C5K9V1, 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, putative n=2 Tax=Perkinsus marinus ATCC 50983 RepID=C5K9V1_PERM5, Expect:2e-15, match=61/176. Blast executed on 2012-01-23 against Uniref90 (Release: 2011_12, 14-Dec-2011) show top hits
• BLASTN TIGR Plant Transcript Assemblies: TA39660_4513, OSJNBb0072N21.7 protein [Oryza sativa (japonica cultivar-group)], Expect:0, match=906/906. Blast executed on 2007-10-23 against TIGR TA Hordeum vulgare release 2 show top hits
• BLASTX NCBI Reference Sequence: XP_002446116, hypothetical protein SORBIDRAFT_06g001950 [Sorghum bicolor], Expect:1e-101, match=183/236. Blast executed on 2010-12-10 against NCBI RefSeq rel-44 show top hits
• BLASTX MSU Rice genome: LOC_Os04g14760.1, phosphoglycerate mutase, putative, expressed, Expect:4e-98, match=178/236. 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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TC212577:weakly similar to UniRef100_A7P8P2 Cluster: Chromosome chr3 scaffold_8, whole genome shotgun sequence; n=1; Vitis vinifera|Rep: Chromosome chr3 scaffold_8, whole genome shotgun sequence - Vitis vinifera (Grape), partial (86%)
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0 |
955/906
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100
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view
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TC222990:similar to UniRef100_A7P8P2 Cluster: Chromosome chr3 scaffold_8, whole genome shotgun sequence; n=1; Vitis vinifera|Rep: Chromosome chr3 scaffold_8, whole genome shotgun sequence - Vitis vinifera (Grape), partial (17%)
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0 |
454/455
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99.8
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view
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TC237454:
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2e-41 |
1096/241
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90.9
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view
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TC226911:similar to UniRef100_UPI0000EB04D6 Cluster: XTP9.; n=1; Canis lupus familiaris|Rep: XTP9. - Canis familiaris, partial (3%)
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2e-35 |
712/234
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89
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view
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TC196681:
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2e-22 |
717/81
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90
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view
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show best hit only
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• BLASTX Brachypodium distachyon genome: Bradi5g03700.1, , Expect:1e-107, match=197/236. Blast executed on 2010-11-03 against Brachypodium distachyon genome, Brachybase release 1 show top hits
• BLASTX Arabidopsis thaliana genome: AT4G38370.1, | Symbols: | Phosphoglycerate mutase family protein | chr4:17970112-17971222 REVERSE LENGTH=226, Expect:7e-71, match=131/219. 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: 906
>Barley1_00039
CAAATGGAGGGTTCGAGCGGCGACTCGCCGCCGGCGCCGCCGCCCGCCTTCCGGAACAGG
TACTGGATCCTCCGCCACGGCCGCAGCGTCCCCAACGAGCGCGGCCTCATCGTCTCCTCC
CTGGAGAACGGCACGAAGCCGGAGTTCGGGCTGGCCCCGGAGGGCGTCGAGCAGGCGCGC
TCCGCCGGCGAGTCGCTCCGGAAGGAGCTTGAGGAGATGGGTGTGCCGGTAGACTCTGTC
AAGATCCGGTATTCGCCGTTCTCGCGGACGACAGAGACGGCCAGGGTGGTCGCTGGTGTG
CTGGGCGTCCCATTTGAGGGTCCTAGCTGCAAGGCAACCGTGGAACTTCGTGAACGTTAT
TTTGGACCATCATATGAGTTGCTTTCACACGAGAAGTATGCAGAGGTATGGGCGATAGAT
GAAGCAGATCCCTTTCTGGCTCCAGAAGGTGGGGAGAGTGTTGCAGATGTTGCTAGTAGA
CTTGCAGGGGTGCTGTCTTCTACAGACGTGGAGTTTCATGGCTCTGCTGTTCTTATTGTC
AGCCATGGGGATCCACTACAGATCTTTCAAGCAGTGCTCAGTGGAGCCAAGGAAAACCCA
TCTTTCCTCGACAAGGTAGCTGGCCTGAAAAAGGAAAGCCTGATAGTTCCATCCGTGTTG
TCGCAGCACCGCAAGTTCGCACTCAACACAGGAGAGCTGCGTCGAGTCGTGTGACCCGAC
ACAGATTTGATCATATGCTCATATGTCGTAGATAATTCATGTATCCGTAATTCCTTATGG
AGAGTCTGATAAGATGGAAAAAATGTTGTTCGATGGCACTCCATTATTTTGGTTGATCAG
ATTGAAGATCTGCTTGTAACCGTGAAAAAAGAGCACATGCACAAGAGATTGCTTTTGAAT
TTGATC
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