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Barley1 22k Microarray Sequence ID: Barley1_00078 |
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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_00078:
Expression details for Contig78_s_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig78_s_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_Os05g06480.1, inorganic H+ pyrophosphatase, putative, expressed, Expect:1e-137, match=256/310. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• Brachypodium distachyon Alignment at Brachybase: Bradi2g34930.1, , Expect:1e-140, match=259/310. 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: 11/04/02 S61424 7e-63 inorganic diphosphatase (EC 3.6.1.1) (clone TVP31) - common tobacco
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Annotation via Blast
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• BLASTX UniProt: UniRef90_Q06572, Pyrophosphate-energized vacuolar membrane proton pump n=15 Tax=Poaceae RepID=AVP_HORVU, Expect:1e-134, match=246/310. Blast executed on 2012-01-23 against Uniref90 (Release: 2011_12, 14-Dec-2011) show top hits
• BLASTN TIGR Plant Transcript Assemblies: TA30924_4513, Vacuolar H+-pyrophosphatase [Oryza sativa (Rice)], Expect:0, match=930/930. Blast executed on 2007-10-23 against TIGR TA Hordeum vulgare release 2 show top hits
• BLASTX NCBI Reference Sequence: NP_001152459, pyrophosphate-energized vacuolar membrane proton pump [Zea mays], Expect:1e-140, match=263/310. Blast executed on 2010-12-10 against NCBI RefSeq rel-44 show top hits
• BLASTX MSU Rice genome: LOC_Os05g06480.1, inorganic H+ pyrophosphatase, putative, expressed, Expect:1e-137, match=256/310. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• BLASTN DFCI Hordeum vulgare Gene Index: TC233532, similar to UniRef100_Q946X5 Cluster: Vacuolar H+-pyrophosphatase; n=1; Prunus persica|Rep: Vacuolar H+-pyrophosphatase - Prunus persica (Peach), partial (68%), Expect:0, match=1556/929. Blast executed on 2010-11-03 against HvGI(DFCI) release 11 show top hits
• BLASTX Brachypodium distachyon genome: Bradi2g34930.1, , Expect:1e-140, match=259/310. 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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AT1G15690.1:| Symbols: AVP1, ATAVP3, AVP-3, AtVHP1;1 | Inorganic H pyrophosphatase family protein | chr1:5399115-5402185 FORWARD LENGTH=771
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1e-133 |
242/310
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78.1
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view
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AT1G15690.2:| Symbols: AVP1, ATAVP3, AVP-3, AtVHP1;1 | Inorganic H pyrophosphatase family protein | chr1:5399115-5402185 FORWARD LENGTH=643
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8e-92 |
170/198
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85.9
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view
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AT1G78920.2:| Symbols: AVP2, AVPL1, AtVHP2;1, VHP2;1, VP2 | vacuolar H+-pyrophosphatase 2 | chr1:29672340-29676761 FORWARD LENGTH=803
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2e-70 |
153/342
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44.7
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view
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AT1G78920.1:| Symbols: AVP2, AVPL1, AtVHP2;1, VHP2;1, VP2 | vacuolar H+-pyrophosphatase 2 | chr1:29672340-29676761 FORWARD LENGTH=803
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2e-70 |
153/342
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44.7
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view
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AT1G16780.1:| Symbols: VHP2;2, AtVHP2;2 | Inorganic H pyrophosphatase family protein | chr1:5739468-5743818 REVERSE LENGTH=852
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5e-70 |
151/342
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44.2
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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: 1150
>Barley1_00078
CCGGTGCAGGCTGTGGCGAACTCATGCCGGACGGGAGCGGCGACGAACGTGATCTTCGGG
CTGGCAGTGGGATACAAGTCGGTCATCGTACCCATCTTCGCCATCGCGACGGCCATCTAC
GCCAGCTTCCGCCTCGCCGCCATGTACGGCATCGCGCTGGCGGCGCTGGGCATGCTCAGC
ACAATCGCCACAGGGCTCAGCATCGACGCCTACGGTCCCATCAGCGACAACGCCGGCGGC
ATCGCCGAGATGTCCGGCATGCCTCACGTGGTCCGCGAGCGCACGGATGCACTCGACGCC
GCCGGTAACACCACCGCCGCCATCGGCAAAGGGTTCGCGATCGGGTCGGCGGCGCTGGTG
TCGCTGGCGCTATTCGGCGCCTACGTGAGCCGCGCCGGGATCGCGGCGGTGGACGTGCTG
AGCCCTCAGGTGTTCGCGGGGCTGCTGGTGGGGGCCATGCTGCCGTACTGGTTCTCGGCG
ATGACCATGCGGAGCGTGGGGAGCGCGGCGCTGGCGATGGTGGAGGAGGTGCGGCGGCAG
TTCGACAGCATCCCGGGGCTGATGGAGGGCACGGCGAAGCCGGACTACGCCACCTGCGTG
AAGATCTCCACCGACGCGTCGCTCAAGAAGATGCTGGCGCCCGGCGCGCTCGTCATGCTG
AGCCCGCTGGTCGCCGGCACGCTGTTCGGCACCGAGACGCTGGCCGGGCTCCTCGCCGGC
GCGCTGGTGTCGGGGGTCCAGGTGGCGATCTCGGCGTCCAACAGCGGCGGCGCGTGGGAC
AACGCCAAGAAGTACATCGAGGCCGGCGCGTCAGCGGAGGCGCGGGCGCTGGGGCCCAAG
GGGTCGGACGCGCACAAGGCGGCCGTGATCGGCGACACCATCGGAGACCCGCTCAAGGAC
ACCTCCGGCCCGTCGCTCAACATCCTCATCTTCAAGCACCTCTGAGTTTGAATTCCGGGT
TCGCGCGTCTTGCTGCCTGGACCTGGATGACCAAGCAGAAGACTTTCGTTACCAATAATA
ATCTCTAGACTGGGAAAATTGTATGAGGTGATGAATGGTTAATGGTTATTTAGTTTCGGA
CTTAATTCGAGTGCAAAACCCGCGTTAGAAAGAAATCAAACTCGTGGTGTTGCAAAAAAA
AAAAAAAAAA
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