 |
|
 |
PLEXdb is committed to making
expression data publicly available to researchers world-wide...
|
|
 |
|
 |
|
|
|
Barley1 22k Microarray Sequence ID: Barley1_00033 |
|
|
|
Sequence Type
|
Exemplar sequence
|
|
Probe Set Details
|
Probe Sequences & Alignment
- Probe sets for Barley1_00033:
Expression details for Contig33_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig33_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_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
|
| Probe Set Annotation
|
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)]
|
|
Annotation via Blast
|
• 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:
|
Subject Sequence Description
|
Expect
|
Identity/Match
|
Identity%
|
HSP
Details
|
|
XP_002463214:hypothetical protein SORBIDRAFT_02g039860 [Sorghum bicolor]
|
1e-29 |
58/86
|
67.4
|
view
|
|
NP_001152002:lipid binding protein [Zea mays]
|
1e-29 |
57/86
|
66.3
|
view
|
|
NP_001060332:Os07g0625800 [Oryza sativa Japonica Group]
|
1e-28 |
55/91
|
60.4
|
view
|
|
NP_001152015:lipid binding protein [Zea mays]
|
2e-27 |
54/80
|
67.5
|
view
|
|
XP_002467775:hypothetical protein SORBIDRAFT_01g033830 [Sorghum bicolor]
|
3e-17 |
44/92
|
47.8
|
view
|
|
show best hit only
|
• 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: 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%), Expect:0, match=1074/850. Blast executed on 2010-11-03 against HvGI(DFCI) release 11 show top hits
• 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.
|
|
Additional Annotations
|
No additional annotations found for this probe set.
|
|
Sequence
|
Total length: 1043
>Barley1_00033
GACCGCCCCCGGACTCCCCCCTCCCCCCCTCCCTCCCGCACTCGAGCACCCACCACCCAC
CATGGCGCGCTCCACCTACTACGCCGTCGCGGCGGTCCTGGCCGTCCTGGCACTGGCGTC
CGGCGCGGCGTCGCAGGCGCCGGCGGCGGGGCCGTCGGCGGACTGCAGCTCCTCGCTCAC
GGGCCTCACCGCCTGCCTCCCCTACATCTCGCCGGGGGCCGCGCCGGGCAAGCCGCCCAA
GGAGTGCTGCGCCGGCGTCAAGGCCGCGCTCGCCAGCCCCGCCAGCGTCGCATGCCTCTG
CGACGCCTTCGGCAAGGACTACGGCATTCCCCTCAACCTCACCCGCGCCAAGGGCCTCCC
CGCCGCCTGCGGCGGCAACCCGGCCGCCCTCAGCAACTGCAGCCTTAAATTGCCCGGCGG
AGCCCCCAATGGCGCCCCTACTGAAGCACCTTCACCAACTTCTGGATCAACACCAACGAC
CGTCAGCCCAAGCCCGTCGAAATCAGCAGCGACCAGATCCCCGGTCTCGGCGGCAACCCT
CGCCCTAGCCGCTATGCCTCTGCTTTCTTACTACTACCTCTGAAGATTTGCCGCATGGTT
TGTTCCATGAATTATTGTCAGTTTAGCTTACTGTTGCCATGAACTATATGAATTCTTGTT
AGCACCAAGTAGTTGTACTATATTTGCATGGTGCCTTCGTCGGAATAAAGTTGATTAGTG
GTGTGCAGATTGATTTTAAAAAAAAAAAAAAAACTCTGTTCCCTGCTCAAGCAGTGTGCT
TGCAGTTAAATGTGTAAACAGGAAGTGCCAATCGGGGGGCCAACTGAACTTGCGCAGATG
CAAGCGTACATCACCAAGGGAAAAAGGCGACGACTCATATTATTTGTGCTTCACCAGATA
GTAGAAACAGATATATAACACTCAGAAAAAGACCAACTCATCATCTGCAGAAAGTGCAGA
GGAGGGAGTTTTGTCAATGAAACAGCACATCACTGGATGATGTATACGAGTTTAAGAATT
GCAGAACAAAAAAAAAAAAAAAA
|
|
|
| | |
