 |
|
 |
PLEXdb is committed to making
expression data publicly available to researchers world-wide...
|
|
 |
|
 |
|
|
|
Barley1 22k Microarray Sequence ID: Barley1_00068 |
|
|
|
Sequence Type
|
Exemplar sequence
|
|
Probe Set Details
|
Probe Sequences & Alignment
- Probe sets for Barley1_00068:
Expression details for Contig68_at
GENE EXPRESSION VARIATION IN EXPERIMENTS for Contig68_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_Os10g40360.1, proline oxidase, mitochondrial precursor, putative, expressed, Expect:7e-65, match=124/140. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• Brachypodium distachyon Alignment at Brachybase: Bradi3g32880.1, , Expect:8e-72, match=132/139. 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 AAG13467.1 3e-86 putative proline oxidase [Oryza sativa (japonica cultivar-group)]
|
|
Annotation via Blast
|
• BLASTX UniProt: UniRef90_Q6NKX1, Proline dehydrogenase 2, mitochondrial n=2 Tax=Arabidopsis RepID=PROD2_ARATH, Expect:2e-40, match=80/129. Blast executed on 2012-01-23 against Uniref90 (Release: 2011_12, 14-Dec-2011) show top hits
• BLASTN TIGR Plant Transcript Assemblies: BM096889, Proline oxidase, putative [Oryza sativa (japonica cultivar-group)], Expect:0, match=581/581. Blast executed on 2007-10-23 against TIGR TA Hordeum vulgare release 2 show top hits
• BLASTX NCBI Reference Sequence: NP_001147660, proline oxidase [Zea mays], Expect:2e-67, match=125/139. Blast executed on 2010-12-10 against NCBI RefSeq rel-44 show top hits
• BLASTX MSU Rice genome: LOC_Os10g40360.1, proline oxidase, mitochondrial precursor, putative, expressed, Expect:7e-65, match=124/140. Blast executed on 2009-08-30 against Rice genome, TIGR release 6.1 show top hits
• BLASTN DFCI Hordeum vulgare Gene Index: BM096889, similar to UniRef100_Q8W415 Cluster: CIG1; n=1; Nicotiana tabacum|Rep: CIG1 - Nicotiana tabacum (Common tobacco), partial (26%), Expect:0, match=581/577. Blast executed on 2010-11-03 against HvGI(DFCI) release 11 show top hits
• BLASTX Brachypodium distachyon genome: Bradi3g32880.1, , Expect:8e-72, match=132/139. Blast executed on 2010-11-03 against Brachypodium distachyon genome, Brachybase release 1 show top hits
• BLASTX Arabidopsis thaliana genome: AT5G38710.1, | Symbols: | Methylenetetrahydrofolate reductase family protein | chr5:15501340-15503899 FORWARD LENGTH=477, Expect:3e-42, match=80/129. 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: 752
>Barley1_00068
GTAATTCAACCTAGTACGAGAGGAACCGTTGATTCACACAATTGGTCATCGCGCTTGGTT
GAAAAGCCAGTGGCGCGAAGCTACCGTGTGCCGGATTATGACTGAACGCCTCTAAGTCAG
AATCCAAGCTAGCATGCGACGCCTGCGCCCGCCGCTCGCCCCGACCCACGTTAGGGGCGC
TGGCGCCCCCACTGGGCCGTGCCGTCGCCGATCCACGGCAGCATCCAGGACACCCACGAC
TGCTACAACGGCTGCGCGGCCTTCCTCCTGGAGCGCGTCCGCCGCGGGTCGGCCTCCGTG
ATGCTGGCCACCCACAACGTGGAGTCCGGGCAGCTGGCGGCGGCGAGGGCGCAGGAGCTT
GGCATCGGCAAGGGCGACCGGAACCTGCAGTTCGCGCAGCTGATGGGCATGGCGGACGGG
CTGTCCCTGGGGCTCCGCAACGCCGGGTTCCAGGTGAGCAAGTACCTGCCCTACGGCCCC
GTGGAGCACATCATCCCCTACCTCATCCGGCGGGCCGAGGAGAACAGAGGACTGCTCTCC
GCTTCCGCGTTCGACAGGCAGCTGCTCCGGAAGGAGCTCGTCAGGAGGTTCAAGAACGCG
GTGATGGGACGGGAGTGAAGCGGGCGGCCGGCCGGCCGGGTGTCCACGTACCGGAGAGAA
GCGATGGAGTTAGAAGTTGTAAATATGCATTGTTGTATCGCGACCTGAATGATGAATGAA
ATAAACGAAATAACCCTAAAAAAAAAAAAAAA
|
|
|
| | |
