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Barley1 GeneChip Exemplar: Barley1_A06498


Name

      

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

Probe sets from Barley1_A06498:
1. A06498.1_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: Q8U6A1, D-nopaline dehydrogenase Length = 413, Expect:0. match=413/413 aa. more

2. BEST BLASTX NR:

3. Artificial sequence for nopaline synthase more

4. BEST BLASTN TIGR Barley Gene Index: CV055135, Length = 617, Expect:1800, match=180/192. 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: 1800
>Barley1_A06498
TGATAGTTTAAACCGAAGGCGGGAAACGACAATCTGATCATGAGCGGAGAATTAAGGGAG
TCACGTTATGACCCCCGCCGATGACGCGGGACAAGCCGTTTTACGTTTGGAACTGACAGA
ACCGCAACGTTGAAGGAGCCACTGAGCCGCGGGTTTCTGGAGTTTAATGAGCTAAGCACA
TACGTCAGAAACCATTATTGCGCGTTCAAAAGTCGCCTAAGGTCACTATCAGCTAGCAAA
TATTTCTTGTCAAAAATGCTCCACTGACGTTCCATAAATTCCCCTCGGTATCCAATTAGA
GTCTCATATTCACTCTCAATCCAAATAATCTGCAATGGCAATTACCTTATCCGCAACTTC
TTTACCTATTTCCGCCGCAGATCACCATCCGCTTCCCTTGACCGTAGGTGTCCTCGGTTC
TGGTCACGCGGGGACTGCATTAGCGGCTTGGTTCGCCTCCCGGCACGTTCCCACGGCGCT
GTGGGCACCAGCAGATCATCCAGGATCGATCTCAGCAATCAAGGCCAGTGAAGGAGTTAT
CACCACCGAGGGAATGATTAACGGTCCATTTAGGGTCTCAGCCTGTGATGACCTTGCCGC
AGTTATTCGCTCCAGCCGTGTACTGATTATTGTAACCCGTGCGGACGTTCACGACAGCTT
CGTCAACGAACTCGCCAACTTCAACGGCGAACTCGCAACAAAGGATATTGTCGTCGTGTG
CGGCCATGGCTTCTCCATCAAGTACGAGAGACAGCTGCGATTCAAGCGAATATTCGAGAC
GGATAATTCGCCCATAACGTCTAAGCTATCGGATCAAAAAAAATGTAACGTCAACATCAA
GGAAATGAAAGCGTCTTTCGGACTGTCATGTTTCCCAATTCATCGCGATGATGCTGGCGT
GATTGATCTACCCGAAGATACCAAGAACATCTTTGCCCAGCTATTTTCCGCTAGAATCAT
CTGCATCCCGCCGTTGCAAGTGCTATTCTTTTCCAACTATATCACTCATGCGGTTCCGGC
AGTCATGAACATCGGAAGACTCCGCGACCCAGCCAATTCTCTTACTAAAAGAGCTGAGAA
GTGGCTTCTTGAACTAGACGAGCGAACCCCACGAGCCGAGAAGGGCTTTTTCTTTTATGG
TGAAGGATCCAACACTTACGTTTGCAACGTCCAAGAGCAAATAGACCACGAACGCCGGAA
GGTTGCCGCAGCGTGTGGACTGCGTCTCAATTCTCTCTTGCAGGAATGCAATGATGAATA
TGATACTGACTATGAAACTTTGAGGGAATACTGCCTAGCACCGTCACCTCATAACGTGCA
TCATGCATGCCCTGACAACATGGAACATCGCTATTTTTCTGAAGAATTATGCTCGTTGGA
GGATGTCGCGGCAATTGCAGCTATTGCCAAAATCGAAATACCCCTCACGCATGCATTCAT
CAATATTATTCATGCGGGGAAAGGCAAGATTAATCCAACTGGCAAATCATCCAGCGTGAT
TGGTAACTTCAGTTCCAGCGACTTGATTCGTTTTGGTGCTACCCACGTTTTCAATAAGGA
CGAGATGGTGGAGTAAAGAAGGAGTGCGTCGAAGCAGATCGTTCAAACATTTGGCAATAA
AGTTTCTTAAGATTGAATCCTGTTGCCGGTCTTGCGATGATTATCATATAATTTCTGTTG
AATTACGTTAAGCATGTAATAATTAACATGTAATGCATGACGTTATTTATGAGATGGGTT
TTTATGATTAGAGTCCCGCAATTATACATTTAATACGCGATAGAAAACAAAATATAGCGC
ESTScan2.0 Prediction ( Arabidopsis model)
 
ESTScan2 CDS Prediction:
Barley1_A06498 88 1 1576 Artificial sequence for nopaline synthase [synthetic construct]
XXTGATAGTTTaAACCGAAGGCGGGAAACGACAATCTGATCATGAGCGGAGAATTAAGGG
AGTCACGTTATGACCCCCGCCGATGACGCGGGACAAGCCGTTTTACgTTTGGAACTGACA
GAACCGCAACGTTGAAGGAGCCACTGAGCCGCGGGTTTCTGGAGTTTAATGAGCTAAGCA
CATACGTCAGAAACCATTATTGCGCGTTCAAAAGTCGCCTAAGGTCACTATCAGCTAGCA
AATATTTCTTGTCAAAAATGCTCCACTGACGTTCCATAAATTCCCCTCGGTATCCAATTA
GAGTCTCATATTCACTCTCAATCCAAAtAATCTGCAATGGCAATTACCTTATCCGCAACT
TCTTTACCTATTTCCGCCGCAGATCACCATCCGCTTCCCTTGACCGTAGGTGTCCTCGGT
TCTGGTCACGCGGGGACTGCATTAGCGGCTTGGTTCGCCTCCCGGCACGTTCCCACGGCG
CTGTGGGCACCAGCAGATCATCCAGGATCGATCTCAGCAATCAAGGCCAGTGAAGGAGTT
ATCACCACCGAGGGAATGATTAACGGTCCATTTAGGGTCTCAGCCTGTGATGACCTTGCC
GCAGTTATTCGCTCCAGCCGTGTACTGATTATTGTAACCCGTGCGGACGTTCACGACAGC
TTCGTCAACGAACTCGCCAACTTCAACGGCGAACTCGCAACAAAGGATATTGTCGTCGTG
TGCGGCCATGGCTTCTCCATCAAGTACGAGAGACAGCTGCGATTCAAGCGAATATTCGAG
ACGGATAATTCGCCCATAACGTCTAAGCTATCGGATCAAAAAAAATGTAACGTCAACATC
AAGGAAATGAAAGCGTCTTTCGGACTGTCATGTTTCCCAATTCATCGCGATGATGCTGGC
GTGATTGATCTACCCGAAGATACCAAGAACATCTTTGCCCAGCTATTTTCCGCTAGAATC
ATCTGCATCCCGCCGTTGCAAGTGCTATTCTTTTCCAACTATATCACTCATGCGGTTCCG
GCAGTCATGAACATCGGAAGACTCCGCGACCCAGCCAATTCTCTTACTAAAAGAGCTGAG
AAGTGGCTTCTTGAACTAGACGAGCGAACCCCACGAGCCGAGAAGGGCTTTTTCTTTTAT
GGTGAAGGATCCAACACTTACGTTTGCAACGTCCAAGAGCAAATAGACCACGAACGCCGG
AAGGTTGCCGCAGCGTGTGGACTGCGTCTCAATTCTCTCTTGCAGGAATGCAATGATGAA
TATGATACTGACTATGAAACTTTGAGGGAATACTGCCTAGCACCGTCACCTCATAACGTG
CATCATGCATGCCCTGACAACATGGAACATCGCTATTTTTCTGAAGAATTATGCTCGTTG
GAGGATGTCGCGGCAATTGCAGCTATTGCCAAAATCGAAATACCCCTCACGCATGCATTC
ATCAATATTATTCATGCGGGGAAAGGCAAGATTAATCCAACTGGCAAATCATCCAGCGTG
ATTGGTAACTTCAGTTCCAGCGACTTGATTCGTTTTGGTGCTACCCACGTTTTCAATAAG
GACGAGATGGTGGAGTAA

Protein Prediction:
DSLTEGGKRQSDHERRIKGVTLXPPPMTRDKPFYFGTDRTATLKEPLSRGFLEFNELSTY
VRNHYCAFKSRLRSLSASKYFLSKMLHXRSINSPRYPIRVSYSLSIQKSAMAITLSATSL
PISAADHHPLPLTVGVLGSGHAGTALAAWFASRHVPTALWAPADHPGSISAIKASEGVIT
TEGMINGPFRVSACDDLAAVIRSSRVLIIVTRADVHDSFVNELANFNGELATKDIVVVCG
HGFSIKYERQLRFKRIFETDNSPITSKLSDQKKCNVNIKEMKASFGLSCFPIHRDDAGVI
DLPEDTKNIFAQLFSARIICIPPLQVLFFSNYITHAVPAVMNIGRLRDPANSLTKRAEKW
LLELDERTPRAEKGFFFYGEGSNTYVCNVQEQIDHERRKVAAACGLRLNSLLQECNDEYD
TDYETLREYCLAPSPHNVHHACPDNMEHRYFSEELCSLEDVAAIAAIAKIEIPLTHAFIN
IIHAGKGKINPTGKSSSVIGNFSSSDLIRFGATHVFNKDEMVE

 

 
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