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Soybean GeneChip Exemplar: Gma.1002.2.S1_at


Name

      

The Soybean Genome Array is a mixed platform contains probe sets for ~37,500 soybean (Glycine max) transcripts, ~ 15,800 Phytophthora sojae transcripts and ~7,500 Heterodera glycines (cyst nematode) transcripts. This page shows annotations for soybean exemplars with prefix"Gma".

Date last modified
2004-11-29
Sequence Type
Consensus sequence from Gma.1002.2
Probe Sets
Probe Sequences & Alignment

Probe sets from Gma.1002.2.S1_at:
1. Gma.1002.2.S1_at:  Expression Details  Probe-Level Intensity
 
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: Q9ZWS2, Flavonoid 3-O-galactosyl transferase Length = 455, Expect:3e-61. match=113/165 aa. more

2. BEST BLASTN TIGR Soybean Gene Index: TC208101, weakly similar to UP|Q9ZWS2 (Q9ZWS2) Flavonoid 3-O-galactosyl transferase, partial (46%) Length = 1022, Expect: 0, match=486/489. It may represent same contig. more

3. BEST TBLASTX Barley1 GeneChip Exemplar: Barley1_18184, Contig1818. (4 members) from HarvEST Triticeae v.1.03 assembly 25 [Hordeum vulgare. (1452 letters), Expect= 2e-34, match=36/66 aa.

4. BEST TBLASTX ATH1 GeneChip Exemplar: 246468_at, ; at|At5g17050; UDP glucose:flavonoid3-o-glucosyltransferase -like protein UDP glucose:flavonoid3-o-glucosyltransferase, Vitis vinifera, EMBL:AF00037. (1383 letters), Expect= 4e-48, match=76/130 aa. more
 
 
BLAST Details

TBLASTX vs Barley1 Exemplars

#

Species

Subject Sequence Description

Expect

Identity/Match

Identity%

HSP
Details

1

barley

Barley1_18184: Contig1818. (4 members) from HarvEST Triticeae v.1.03 assembly 25 [Hordeum vulgare. (1452 letters)

2e-34

36/66

54

View
Nucleotide Sequence
 
Total length: 489

>Gma.1002.2.S1_at gb|AW471508; /DB_XREF=si12a12.y1 /CLONE=GENOME SYSTEMS CLONE ID: Gm-c1029-983
ctaaggtagtagttatgaatttctttgaggaattggaaccacctttgtttgttcaagaca
tgagaaacaagttgcagtctttgctttatgttgttccacttccttccacgttgttgccac
catctgacacagattcaagtggttgcttgtcatggttgggtatgaagaactctaaatcgg
tggcttatgtttgctttgggactgtggnggcaccacctccacatgagcttgtggcagtgg
cagaggcattggaagaaagtggctttccttttctgtggtctctgaaggaaggtctaatga
gtcttttgccaaatgggtttgttgagaggaccaagaagcgtgggaaaatagtgtcttggg
ctccacaaacccatgttttggctcatgattctgtaggagtttttgtgactcactgtggag
ctaactctgtgattgagagtgtttccagtggtgtgactatgatctgcaggccattctttg
gagatcaag

 

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