 |
|
 |
PLEXdb is committed to making
expression data publicly available to researchers world-wide...
|
|
 |
|
 |
|
|
|
Barley1 22k Microarray Sequence ID: Barley1_00078 |
|
|
|
Sequence Type
|
Exemplar sequence
|
|
Probe Set Details
|
Probe Sequences & Alignment
- Probe sets for Barley1_00078:
Expression details for Contig78_s_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig78_s_at
|
|
Alignments and Assemblies
|
• 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
|
|
Model Genome Alignments
|
• 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
|
| Probe Set Annotation
|
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
|
|
Annotation via Blast
|
• 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:
|
Subject Sequence Description
|
Expect
|
Identity/Match
|
Identity%
|
HSP
Details
|
|
NP_001152459:pyrophosphate-energized vacuolar membrane proton pump [Zea mays]
|
1e-140 |
263/310
|
84.8
|
view
|
|
XP_002440641:hypothetical protein SORBIDRAFT_09g004450 [Sorghum bicolor]
|
1e-138 |
261/310
|
84.2
|
view
|
|
NP_001054701:Os05g0156900 [Oryza sativa Japonica Group]
|
1e-137 |
256/310
|
82.6
|
view
|
|
NP_001056966:Os06g0178900 [Oryza sativa Japonica Group]
|
1e-135 |
248/310
|
80
|
view
|
|
XP_002512502:Pyrophosphate-energized vacuolar membrane proton pump, putative [Ricinus communis]
|
1e-135 |
247/310
|
79.7
|
view
|
|
show best hit only
|
• 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: AT1G15690.1, | Symbols: AVP1, ATAVP3, AVP-3, AtVHP1;1 | Inorganic H pyrophosphatase family protein | chr1:5399115-5402185 FORWARD LENGTH=771, Expect:1e-133, match=242/310. 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.
|
|
Additional Annotations
|
No additional annotations found for this probe set.
|
|
Sequence
|
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
|
|
|
| | |
