 |
|
 |
PLEXdb is committed to making
expression data publicly available to researchers world-wide...
|
|
 |
|
 |
|
|
|
Barley1 22k Microarray Sequence ID: Barley1_00003 |
|
|
|
Sequence Type
|
Exemplar sequence
|
|
Probe Set Details
|
Probe Sequences & Alignment
- Probe sets for Barley1_00003:
Expression details for Contig3_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig3_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_Os07g11510.1, RAL6 - Seed allergenic protein RA5/RA14/RA17 precursor, expressed, Expect:4e-19, match=48/120. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• Brachypodium distachyon Alignment at Brachybase: Bradi1g54000.1, , Expect:5e-18, match=49/133. 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: 11/06/02 P13691 9e-69 ALPHA-AMYLASE INHIBITOR BDAI-I PRECURSOR pir||S00332 alpha-amylase inhibitor precursor (clone pUP-44) - barley
|
|
Annotation via Blast
|
• BLASTX UniProt:
|
Subject Sequence Description
|
Expect
|
Identity/Match
|
Identity%
|
HSP
Details
|
|
UniRef90_P13691:Alpha-amylase inhibitor BDAI-1 n=3 Tax=Hordeum vulgare RepID=IAA2_HORVU
|
7e-62 |
111/123
|
90.2
|
view
|
|
UniRef90_P01083:Alpha-amylase inhibitor 0.28 n=114 Tax=Triticeae RepID=IAA2_WHEAT
|
8e-39 |
75/121
|
62
|
view
|
|
UniRef90_P16968:Alpha-amylase inhibitor BMAI-1 (Fragment) n=2 Tax=Triticeae RepID=IAA1_HORVU
|
3e-23 |
55/122
|
45.1
|
view
|
|
UniRef90_P01085:Alpha-amylase inhibitor 0.19 n=124 Tax=Triticeae RepID=IAA1_WHEAT
|
2e-19 |
51/111
|
45.9
|
view
|
|
UniRef90_Q01881:Seed allergenic protein RA5 n=3 Tax=Oryza sativa RepID=RA05_ORYSJ
|
1e-17 |
47/116
|
40.5
|
view
|
|
show best hit only
|
• BLASTN TIGR Plant Transcript Assemblies: TA30520_4513, Alpha-amylase inhibitor BDAI-I precursor [Hordeum vulgare (Barley)], Expect:0, match=528/528. Blast executed on 2007-10-23 against TIGR TA Hordeum vulgare release 2 show top hits
• BLASTX NCBI Reference Sequence: NP_001059189, Os07g0215500 [Oryza sativa Japonica Group], Expect:2e-18, match=48/120. Blast executed on 2010-12-10 against NCBI RefSeq rel-44 show top hits
• BLASTX MSU Rice genome: LOC_Os07g11510.1, RAL6 - Seed allergenic protein RA5/RA14/RA17 precursor, expressed, Expect:4e-19, match=48/120. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• BLASTN DFCI Hordeum vulgare Gene Index: TC235364, UniRef100_P13691 Cluster: Alpha-amylase inhibitor BDAI-1 precursor; n=2; Hordeum vulgare|Rep: Alpha-amylase inhibitor BDAI-1 precursor - Hordeum vulgare (Barley), complete, Expect:0, match=751/633. Blast executed on 2010-11-03 against HvGI(DFCI) release 11 show top hits
• BLASTX Brachypodium distachyon genome: Bradi1g54000.1, , Expect:5e-18, match=49/133. Blast executed on 2010-11-03 against Brachypodium distachyon genome, Brachybase release 1 show top hits
• BLASTX Arabidopsis thaliana genome: No 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: 721
>Barley1_00003
TAATCAAAAATAACCGATAATATTTCTTAAGCCGAAGATAGTAAGAGTGTAGCTACCGAT
CGATATAAGCAACTGATTAAGATAGTAGTAGATGGGAATGGGAGCAATGTGGATGAAGAG
CATGTTGTTGGTGCTCCTGCTATGCATGCTCATGGTGACTCCAATGACGGGCGCACGGAG
TGATAACAGTGGCCCTTGGATGTGGTGTGATCCTGAGATGGGCCACAAGGTGAGCCCGCT
CACGCGCTGCCGAGCATTGGTGAAGCTCGAGTGTGTGGGCAACCGGGTGCCCGAGGATGT
CCTAAGAGACTGCTGCCAGGAGGTGGCCAACATCAGCAACGAGTGGTGCAGGTGCGGCGA
CCTCGGCAGCATGCTGCGCAGCGTGTATGCGGCGCTCGGCGTGGGGGGCGGACCGGAGGA
GGTGTTCCCGGGTTGCCAGAAGGATGTGATGAAGCTCTTGGTTGCAGGCGTGCCTGCGCT
CTGCAATGTCCCCATTCCCAACGAGGCGGCAGGCACCAGAGGGGTCTGCTACTGGTCAGC
GTCTACGGACACCTAGTCAAGCGATTATTATGCTTTTTAATAATTTGTGTGGTGTGTGTG
TGCGCGCACAAGATGAATAAAATGAAATAATGGTGTATCTGCCAAAAAAAAAAAAAAAAA
ATGTATGAACCTGAACTTAATTTAATTTTCCTACTCATAGATAAAAAAAAAAAAAAAAAA
A
|
|
|
| | |
