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Sugarcane 8K GeneChip Exemplar: Sof.1126.2.S1_at


Name

      

Date last modified
2005-07-04
Sequence Type
Consensus sequence from Sof.1126.2
Probe Sets
Probe Sequences & Alignment

Probe sets from Sof.1126.2.S1_at:
1. Sof.1126.2.S1_at:  Expression Details Probe-Level Intensity
 
Genome Alignment

 
BLAST and EST alignment

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

Annotation 
1. BEST BLASTX UniProt: Q5Z6I7_ORYSA, (Q5Z6I7) Embryogenesis transmembrane protein-like Length = 968, Expect:2e-84. match=188/398 aa. more

2. BEST BLASTN TIGR Sugarcane 8K Gene Index: TC50516, weakly similar to UP|O24564 (O24564) Embryogenesis transmembrane protein, partial (18%) Length = 2128, Expect: 0, match=646/661. It may represent same contig. more

3. BEST TBLASTX Barley1 GeneChip Exemplar: Barley1_49972, Contig49972 (1 member:rbags23g22) from HarvEST Triticeae v. 1.03 assembly 25 [Hordeum vulgare] Length = 656, Expect= 1e-35, match=61/133 aa.

4. BEST TBLASTX ATH1 GeneChip Exemplar: 254948_at, |At4g11000 putative protein various predicted proteins, Arabidopsis thaliana Length = 1221, Expect= 7e-06, match=18/33 aa. more
 
 
BLAST Details

TBLASTX vs Barley1 Exemplars

#

Species

Subject Sequence Description

Expect

Identity/Match

Identity%

HSP
Details

1

barley

Barley1_49972: Contig49972 (1 member:rbags23g22) from HarvEST Triticeae v. 1.03 assembly 25 [Hordeum vulgare] Length = 656

1e-35

61/133

45

View

2

barley

Barley1_24322: Contig24322 (2 members) from HarvEST Triticeae v. 1.03 assembly 25 [Hordeum vulgare] Length = 630

1e-30

55/101

54

View
Nucleotide Sequence
 
Total length: 1164

>Sof.1126.2.S1_at gb|CA163321
cctcgccggcgacccaatccttcacataacctatccccagagatacctggctttcttcta
ctgcaacgcgacagctttcgtcgcatcgctggttatcctgatcctcctcctaagcagcac
attcagcacccaaggaatcaagtactacgcactgcaggtcgccatgatcctggaccttct
tgggctgattggcgcctatgctgccgggagttgcaagcaagtgtccaaatccgtgtacat
ctcggtcattgtggttccagtgttcctctatgttggcatccatgttctggtgttcatgct
tgaagtcttcccaaatcatgccacatggagggagatgctgaaggacaagctggagaagtc
catccccgaatggctcaagaagttgtttgagccacagaccgaggaggaagatgaggaaat
gaaatggaaattggagaagagccgcaagctcctactgctccttgccattcttgcagcagg
cctcacataccangccggcatgagtcccccgggcggcttctggcaacagaacaagacagg
ccatctcattggcaacccagtgctcaatgacaactacccacgtcgttacctngnnnncnt
nnnctgcaatgcaactgccttcgttgcatctctggccatcatcatgctgctggttaacag
nannnnnnngnnnnannnnnnnnnnnnctatgcactcagngtgtgcgtgatccttgacct
ggttgggctcatgggtgcgtntgctgcagggngctccaggaaggtatncacatccatata
tgtcttcgtcctggtctttgcagttctaatatgcatcgnnctccaagttattctggttgt
gtcnnagtcgnttcagggtctcttgcagagactcctgtccttcntcgangtaanagagga
ngaagctggtgacacattgccgcatacagctgctgatncagaggcacaagatccctggta
taagaagttgcccaaatacntgttgctnctngcngcacttgcagcngctgtcacttacca
agccgccatgaacccncccggtgggctctggggcganggncaaantgnccacatagctgg
tgatccagttcttnggagcacctatccacgccgttataaggccttcttctactgcaacgc
gactttctttatggcttctctggt

 

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