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Barley1 22k Microarray Sequence ID: Barley1_00033 |
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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_00033:
Expression details for Contig33_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig33_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_Os07g43290.1, LTPL56 - Protease inhibitor/seed storage/LTP family protein precursor, expressed, Expect:3e-29, match=55/91. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• Brachypodium distachyon Alignment at Brachybase: Bradi1g20670.1, , Expect:2e-31, match=57/86. 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 BAC07063.1 4e-29 (AP004009) hypothetical protein~predicted by FGENESH etc. [Oryza sativa (japonica cultivar-group)]
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Annotation via Blast
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• BLASTX UniProt: UniRef90_Q6ASY2, Non-specific lipid transfer protein-like 1 n=2 Tax=Oryza sativa RepID=NLTL1_ORYSJ, Expect:3e-14, match=41/87. Blast executed on 2012-01-23 against Uniref90 (Release: 2011_12, 14-Dec-2011) show top hits
• BLASTN TIGR Plant Transcript Assemblies: TA30871_4513, Hypothetical protein OJ1339_F05.116 [Oryza sativa (japonica cultivar-group)], Expect:0, match=700/700. Blast executed on 2007-10-23 against TIGR TA Hordeum vulgare release 2 show top hits
• BLASTX NCBI Reference Sequence: XP_002463214, hypothetical protein SORBIDRAFT_02g039860 [Sorghum bicolor], Expect:1e-29, match=58/86. Blast executed on 2010-12-10 against NCBI RefSeq rel-44 show top hits
• BLASTX MSU Rice genome: LOC_Os07g43290.1, LTPL56 - Protease inhibitor/seed storage/LTP family protein precursor, expressed, Expect:3e-29, match=55/91. 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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TC208430:similar to UniRef100_A2YLE0 Cluster: Non-specific lipid-transfer protein; n=1; Oryza sativa Indica Group|Rep: Non-specific lipid-transfer protein - Oryza sativa subsp. indica (Rice), partial (22%)
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0 |
1074/850
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100
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view
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TC218168:weakly similar to UniRef100_A7P9F6 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 (13%)
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0 |
805/621
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99.5
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view
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CA024613:homologue to UniRef100_P62945 Cluster: 60S ribosomal protein L41; n=13; Eukaryota|Rep: 60S ribosomal protein L41 - Homo sapiens (Human), complete
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4e-64 |
451/130
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98.5
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view
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show best hit only
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• BLASTX Brachypodium distachyon genome: Bradi1g20670.1, , Expect:2e-31, match=57/86. Blast executed on 2010-11-03 against Brachypodium distachyon genome, Brachybase release 1 show top hits
• BLASTX Arabidopsis thaliana genome: AT5G64080.2, | Symbols: | Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein | chr5:25645475-25646638 REVERSE LENGTH=179, Expect:9e-12, match=35/92. 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: 1043
>Barley1_00033
GACCGCCCCCGGACTCCCCCCTCCCCCCCTCCCTCCCGCACTCGAGCACCCACCACCCAC
CATGGCGCGCTCCACCTACTACGCCGTCGCGGCGGTCCTGGCCGTCCTGGCACTGGCGTC
CGGCGCGGCGTCGCAGGCGCCGGCGGCGGGGCCGTCGGCGGACTGCAGCTCCTCGCTCAC
GGGCCTCACCGCCTGCCTCCCCTACATCTCGCCGGGGGCCGCGCCGGGCAAGCCGCCCAA
GGAGTGCTGCGCCGGCGTCAAGGCCGCGCTCGCCAGCCCCGCCAGCGTCGCATGCCTCTG
CGACGCCTTCGGCAAGGACTACGGCATTCCCCTCAACCTCACCCGCGCCAAGGGCCTCCC
CGCCGCCTGCGGCGGCAACCCGGCCGCCCTCAGCAACTGCAGCCTTAAATTGCCCGGCGG
AGCCCCCAATGGCGCCCCTACTGAAGCACCTTCACCAACTTCTGGATCAACACCAACGAC
CGTCAGCCCAAGCCCGTCGAAATCAGCAGCGACCAGATCCCCGGTCTCGGCGGCAACCCT
CGCCCTAGCCGCTATGCCTCTGCTTTCTTACTACTACCTCTGAAGATTTGCCGCATGGTT
TGTTCCATGAATTATTGTCAGTTTAGCTTACTGTTGCCATGAACTATATGAATTCTTGTT
AGCACCAAGTAGTTGTACTATATTTGCATGGTGCCTTCGTCGGAATAAAGTTGATTAGTG
GTGTGCAGATTGATTTTAAAAAAAAAAAAAAAACTCTGTTCCCTGCTCAAGCAGTGTGCT
TGCAGTTAAATGTGTAAACAGGAAGTGCCAATCGGGGGGCCAACTGAACTTGCGCAGATG
CAAGCGTACATCACCAAGGGAAAAAGGCGACGACTCATATTATTTGTGCTTCACCAGATA
GTAGAAACAGATATATAACACTCAGAAAAAGACCAACTCATCATCTGCAGAAAGTGCAGA
GGAGGGAGTTTTGTCAATGAAACAGCACATCACTGGATGATGTATACGAGTTTAAGAATT
GCAGAACAAAAAAAAAAAAAAAA
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