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Barley1 GeneChip Exemplar: Barley1_00003


Name

      

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

Probe sets from Barley1_00003:
1. Contig255_at:  Expression Details  Probe-Level Intensity
2. Contig3_at:  Expression Details  Probe-Level Intensity
3. HF19N13r_s_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: IAA2_HORVU, (P13691) Alpha-amylase inhibitor BDAI-I precursor Length = 152, Expect:2e-88. match=152/152 aa. more

2. BEST BLASTX NR: P13691, ALPHA-AMYLASE INHIBITOR BDAI-I PRECURSOR pir||S00332 alpha-amylase inhibitor precursor (clone pUP-44) - barley , Expect:3e-88.

3. BEST BLASTX PLANTS: 10/14/03 1. sp|P13691 5e-089 IAA2_HORVU ALPHA-AMYLASE INHIBITOR BDAI-I PRECURSOR Length = 152; 2. S00332 5e-089 pir|| alpha-amylase inhibitor precursor (clone pUP-44) - barley Length = 152; 3. emb|CAA08836.1 5e-089 BDAI-1; Barley dime more

4. BEST BLASTN TIGR Barley Gene Index: TC146614, UP|IAA2_HORVU (P13691) Alpha-amylase inhibitor BDAI-I precursor, complete Length = 706, Expect: 721, match=581/581. 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: 721
>Barley1_00003
TAATCAAAAATAACCGATAATATTTCTTAAGCCGAAGATAGTAAGAGTGTAGCTACCGAT
CGATATAAGCAACTGATTAAGATAGTAGTAGATGGGAATGGGAGCAATGTGGATGAAGAG
CATGTTGTTGGTGCTCCTGCTATGCATGCTCATGGTGACTCCAATGACGGGCGCACGGAG
TGATAACAGTGGCCCTTGGATGTGGTGTGATCCTGAGATGGGCCACAAGGTGAGCCCGCT
CACGCGCTGCCGAGCATTGGTGAAGCTCGAGTGTGTGGGCAACCGGGTGCCCGAGGATGT
CCTAAGAGACTGCTGCCAGGAGGTGGCCAACATCAGCAACGAGTGGTGCAGGTGCGGCGA
CCTCGGCAGCATGCTGCGCAGCGTGTATGCGGCGCTCGGCGTGGGGGGCGGACCGGAGGA
GGTGTTCCCGGGTTGCCAGAAGGATGTGATGAAGCTCTTGGTTGCAGGCGTGCCTGCGCT
CTGCAATGTCCCCATTCCCAACGAGGCGGCAGGCACCAGAGGGGTCTGCTACTGGTCAGC
GTCTACGGACACCTAGTCAAGCGATTATTATGCTTTTTAATAATTTGTGTGGTGTGTGTG
TGCGCGCACAAGATGAATAAAATGAAATAATGGTGTATCTGCCAAAAAAAAAAAAAAAAA
ATGTATGAACCTGAACTTAATTTAATTTTCCTACTCATAGATAAAAAAAAAAAAAAAAAA
A
ESTScan2.0 Prediction ( Arabidopsis model)
 
ESTScan2 CDS Prediction:
Barley1_00003 -12 157 695 contig from HarvEST v. 1.03 assembly 25 [Hordeum vulgare]; minus strand
ATCGCTTGACTAGGTGTCCGTAGACGCTGACCAGTAGCAGACCCCTCTGGTGCCTGCCGC
CTCGTTGGGAATGGGGACATTGCAGAGCGCAGGCACGCCTGCAACCAAGAGCTTCATCAC
ATCCTTCTGGCAACCCGGGAACACCTCCTCCGGTCCGCCCCCCACGCCGAGCGCCGCATA
CACGCTGCGCAGCATGCTGCCGAGGTCGCCGCACCTGCACCACTCGTTGCTGATGTTGGC
CACCTCCTGGCAGCAGTCTCTTAGGACATCCTCGGGCACCCGGTTGCCCACACACTCGAG
CTTCACCAATGCTCGGCAGCGCGTGAGCGGGCTCACCTTGTGGCCCATCTCAGGATCACA
CCACATCCAAGGGCCACTGTTATCACTCCGTgCGCCCGTCATTGGAGTCACCATGAGCAT
GCATAGCAGGAGCACCAACAACATGCTCTTCATCCACATTGCTCCCATTCCCATCTACTA
CTATCTTAATCAGTTGCTTATATCGATCGGTAGCTACACTCTTACTaTCTTCGGCTTAA

Protein Prediction:
IAXLGVRRRXPVADPSGACRLVGNGDIAERRHACNQELHHILLATREHLLRSAPHAERRI
HAAQHAAEVAAPAPLVADVGHLLAAVSXDILGHPVAHTLELHQCSAARERAHLVAHLRIT
PHPRATVITPSPVIGVTMSMHSRSTNNMLFIHIAPIPIYYYLNQLLISIGSYTLTSSA

 

 
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