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Barley1 GeneChip Exemplar: Barley1_00360


Name

      

Date last modified
2004-12-04
Sequence Type
Exemplar
Probe Sets
Probe Sequences & Alignment

Probe sets from Barley1_00360:
1. Contig360_x_at:  Expression Details  Probe-Level Intensity
 
Genomic Alignment with
Rice and Cereals		No Rice Alignment at Gramene
BLAST and EST alignment
Plant Sequence BLAST

1. PlantGDB  2. BarleyBase Blast 3. NCBI BLAST  4. GrainGenes BLAST on Mapped Wheat Ests etc 5. Gramene BLAST  6. EBI BLAST 7. TAIR BLAST  

Annotation 
1. BEST BLASTX UniProt:

2. BEST BLASTX NR: S53050, "RNA binding protein - barley emb|CAA88558.1| glycine rich protein, RNA binding protein [Hordeum vulgare subsp." , Expect:1e-100.

3. BEST BLASTX NR: more

4. BEST BLASTN TIGR Barley Gene Index: TC138719, homologue to UP|Q41518 (Q41518) Single-stranded nucleic acid binding protein, partial (81%) Length = 876, Expect: 205, match=188/188. It may represent same contig. more

5. BEST TBLASTX ATH1 GeneChip Exemplar:

Barley1 exemplars and BEST BLASTX NR results are kindly provided by Dr. Timothy Close from  HarvEST:Barley. BLASTX NR is based on contig assembly #31, and other BLASTs are based on contig assembly #25 from HarvEST:Barley.

     up to 5 BLAST top hits for all types of BLASTs.
Nucleotide Sequence
 
Total length: 205
>Barley1_00360
GACCCCGTCTCATCGCCCAGTTATCCATCCATCTATCGTCTACCGTCTTCGTCAGCAAGT
TATCTATCTTCGGTGTGTCAGTCTGAGTCGTGTTTGTGTGTCTGTCCGGTCCTGTGGTGT
TTTTGATCGCGAGCTCGAGTGGTCTCTGTGTTACGCGAGGAAGAAACAACATGTCTTATC
TTTCAGTCAAAAAAAAAAAAAAAAA
ESTScan2.0 Prediction ( Arabidopsis model)
 
ESTScan2 CDS Prediction:
Barley1_00360 58 34 205 contig from HarvEST v. 1.03 assembly 25 [Hordeum vulgare]; minus strand
ATGTTGTTTCTTCCTCGCGTAACACAGAGACCACTCGAGCTCGCGATCAAAAACACCACA
GGACCGGACAGACACACAAACACGACTCAGACTGACACACCGAAGATAGATAACTTGCTG
ACGAAGACGGTAGACGATAGATGGATGGATAACTGGGCGATGAGACGGGGTCXX

Protein Prediction:
MLFLPRVTQRPLELAIKNTTGPDRHTNTTQTDTPKIDNLLTKTVDDRWMDNWAMRRGX

 

 
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