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Rice GeneChip Exemplar: Os.10220.1.S1_at


Name

      

Date last modified
2005-01-10
Sequence Type
Consensus sequence from Os.10220.1
Probe Sets
Probe Sequences & Alignment

Probe sets from Os.10220.1.S1_at:
1. Os.10220.1.S1_at:  Expression Details  Probe-Level Intensity
 
Rice Genome AlignmentGenome Alignment at Gramene

On the Gramene entry page, under the "Location of hits" section, select one of the locations to go to the genome browser (ContigView) page, then under "Detailed view" section, select "arrays" menu and check the platforms to be displayed.
BLAST and EST alignment
Plant Sequence BLAST

 1. BarleyBase Blast  2. NCBI BLAST  3. EBI BLAST 4. GrainGenes BLAST  5. Gramene BLAST  6. TAIR BLAST  

Annotation 
1. BEST BLASTX UniProt:
BLASTX result for this exemplar against UniProt will be available soon. You may try BLAST at EBI


2. BEST BLASTN TIGR Rice Gene Index: TC250680, UP|Q7X993 (Q7X993) BZIP transcription factor, complete Length = 2209, Expect: 0, match=2189/2196. It may represent same contig. more

3. BEST TBLASTX Barley1 GeneChip Exemplar: Barley1_05907, Contig5907 (9 members) from HarvEST Triticeae v. 1.03 assembly 25 [Hordeum vulgare] Length = 1308, Expect= 0, match=215/232 aa.

4. BEST TBLASTX ATH1 GeneChip Exemplar: 250671_at, ; |At5g06950; transcription factor HBP-1b homolog (sp|P43273) ; supported by cDNA: gi_217826_dbj_D10042.1_ATHAHBP1B Length = 993, Expect= 0, match=242/322 aa. more
 
 
BLAST Details

TBLASTX vs Barley1 Exemplars

#

Species

Subject Sequence Description

Expect

Identity/Match

Identity%

HSP
Details

1

barley

Barley1_05907: Contig5907 (9 members) from HarvEST Triticeae v. 1.03 assembly 25 [Hordeum vulgare] Length = 1308

0

215/232

92

View

2

barley

Barley1_05909: Contig5909 (14 members) from HarvEST Triticeae v. 1.03 assembly 25 [Hordeum vulgare] Length = 1687

0

182/244

74

View

3

barley

Barley1_16432: Contig16432 (5 members) from HarvEST Triticeae v. 1.03 assembly 25 [Hordeum vulgare] Length = 1419

0

85/143

59

View

4

barley

Barley1_11819: Contig11819 (6 members) from HarvEST Triticeae v. 1.03 assembly 25 [Hordeum vulgare] Length = 1677

4e-56

58/106

54

View

5

barley

Barley1_36667: Contig36667 (1 member:HR01L10r) from HarvEST Triticeae v. 1.03 assembly 25 [Hordeum vulgare] Length = 419

2e-14

32/51

62

View
Nucleotide Sequence
 
Total length: 2207

>Os.10220.1.S1_at gb|AB051295.1
ctctctccacctcctccactctcccaccacnacgagaccttctcgangcttcctcccccc
caaaccccttccgctcctcctcctcctcccaaatccaccacggcgacgccgccgccgcag
agcccctagctcccggaggtccctcgcccccgccagctccgacggcctcacggaaggagg
agtaacgtgggcgttgattggatttttttgttttccccccaccttgagtgagtctgtgcc
gtttccccggcggcgagggagggcagagggctgatcatggtcgtgcgccgccggtgcctt
gccgagatttcccccaaccgccaccgacgatcgttcacttggcacaaaggggagtagcac
tgtccaagctgttgtggtccgtcagggagattggccaacctgtggggtttcagatcgaca
taagtacgtcagtatttcagccatcgatcaatctggcggttcatagggctgtgcttgcaa
cctttctggcagaaaggagagagcaaagtgatttgctgtctcctgttgattgtggcctgt
tgaggcccagtaatggcagatgctagttcaaggactgacacatcgattgttgtagacaac
gacgacaaaaaccaccagttagaaaacggacatagtggtgcagtcatggcttctaactct
tcagatagatctgacagatctgacaaacttatggaccaaaagacaattcggcggcttgct
caaaatcgtgaggcagcaagaaaaagtcggctgaggaaaaaggcatatgtgcaacaacta
gagagcagtaagctgaagcttgcacagctagagcaggaacttcagaaagctcgtcagcag
ggaatcttcatctctagctctggagaccagacccatgccatgagtggaaatggggcattg
acttttgacttagaatacactagatggctcgaggagcaaaataagcagataaatgagttg
aggacagcagtgaatgctcatgcaagtgacagtgaccttcgtcttattgttgatggcata
atggcgcattatgacgaggtattcaaggttaagggtgtagctgcaaaggccgatgtgttt
catatactttcaggcatgtggaagacacccgcagaaagatgcttcctgtggcttggtggt
ttccgtccatctgagcttctaaagctcctagcaaatcacctcgaacctttaaccgagcag
cagttgctgggattaaacaacctccaggaatcttctcagcaggcggaggatgcactttca
caaggtatggaagcactgcagcaatctctggcagatactttggctggatctctcgnttca
tcagggtcttctgggaatgtggcgaactacatgggtcagatggcaatggccatgggtaaa
ctaggaacgctcgagaatttcctttgccaggcggacaacctgcgacagcagacattgcat
caaatgcaacgaattctgacgatccggcaagcctcgcgtgctcttcttgccatacacgat
tacttttcacgcttgcgtgctttgagttcgctgtggcttgctaggccacgggagtaacaa
aatggtcatgtgtgcctgtgacgaggttagacgctcattttgatggacngcagataattg
ggtttttccctgtacaattgtgtttggcagctgtggagctaaagttaaaaactgtaccta
aagtggtgtatgcaaataggtgaagcctctaagtaagttataacgattgcattattgtgt
tagcaataaaagttgggtaattcaggatgtgtcctgagttgttttgttgtagtagaagaa
ctgcatgtagtggctggaaatgcagtgttgaatgtaactaaagctctgctgctcacgttg
cataatgttgtgtagtaatagttagctagtgatgcccattttacctgcactcctctggga
agctgaaactgcaacctgaagcaaccacggtgcagaagaccgcatgcatggtaaatgatt
aaaaggatatatatgggctcaacatcgctgccaaatcctgagataatgaacaggcatgct
aaactgctacttccacatgaaacntcccagttgacatgaagaatgagctgttcagtttta
tggtttctgtgttgcactgtacataattcctgtacgggtctgaanttatcctgaaatcat
gctaaactgcagaagcatatgaaatctccagaccggntgacatgaaa

 

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