Hello! Guest! Please Login or Register! Log Out

Barley1 GeneChip Exemplar: Barley1_00796


Name

      

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

Probe sets from Barley1_00796:
1. Contig796_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: THNA_HORVU, (P01545) Alpha-hordothionin precursor (Purothionin II) Length = 127, Expect:3e-36. match=70/70 aa. more

2. BEST BLASTX NR: , , Expect:0.

3. BEST BLASTX PLANTS: 10/14/03 1. VSBH2 8e-037 pir|| alpha-hordothionin precursor - barley Length = 133; 2. gb|AAA32966.1 8e-037 alpha-hordothionin Length = 133; 3. sp|P01545 8e-037 THNA_HORVU Alpha-hordothionin precursor (Purothionin II) Length = 127; more

4. BEST BLASTN TIGR Barley Gene Index: TC146372, homologue to UP|HOR3_HORVU (P06471) B3-hordein (Fragment), partial (88%) Length = 1535, Expect: 520, match=377/379. 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: 520
>Barley1_00796
TGGAGACCTTTTCTTATCATTAGACACCAACACTGGGACCAACGCCTCGCAGGATCTTGT
ACAACGGCACATTAACACTGCACATCGTTGGTAGGGTGCGCAGCGCAATGAAACCTCGTG
AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCC
TCGTGCCAATTCGGCACGAGGGCCCTACAGGCTTCCCCAAATTGGCCCTTGTGTCCAACT
CAGATGAACCAGACACCGTCAAGTATTGCAACTTGGGGTGTAGGGCTTCCATGTGTGACT
ACATGGTCAACGCAGCTGCTGACGACGAAGAAATGAAACTCTATTTGGAAAATTGTGGTG
ATGCTTGTGTCAATTTCTGCAACGGTGATGCTGGCCTCACATCCCTTACTGCCTAATGAT
GTGTATCCATGGTCTGAGATTTCACAGGGCAAGGTGTGTCTGACCTTTGCGTTCAATAAA
ATTGGATCCCATCGAGAGTATCCAAAAAAAAAAAAAAAAA
ESTScan2.0 Prediction ( Arabidopsis model)
 
ESTScan2 CDS Prediction:
Barley1_00796 186 199 416 contig from HarvEST v. 1.03 assembly 25 [Hordeum vulgare]
AGGGCCCTXACAGGCTTCCCCAAATTGGCCCTTGTGTCCAACTCAGATGAACCAGACACC
GTCAAGTATTGCAACTTGGGGTGTAGGGCTTCCATGTGTGACTACATGGTCAACGCAGCT
GCTGACGACGAAGAAATGAAACTCTATTTGGAAAATTGTGGTGATGCTTGTGTCAATTTC
TGCAACGGTGATGCTGGCCTCACATCCCTTACTGCCTAA

Protein Prediction:
RALTGFPKLALVSNSDEPDTVKYCNLGCRASMCDYMVNAAADDEEMKLYLENCGDACVNF
CNGDAGLTSLTA

 

 
Copyright@2001-2005 The BarleyBase Group
All rights reserved.

For problems with the webpages, contact barleybasewebmaster