Barley1 GeneChip Exemplar: Barley1_01508
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Name
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Date last modified
| 2004-12-04 |
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Sequence Type
| Exemplar
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Probe Sets
| Probe Sequences & Alignment
Probe sets from Barley1_01508:
1. Contig1508_s_at: Expression Details Probe-Level Intensity
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Genomic Alignment with
Rice and Cereals | Genome Alignment at Gramene
On the Gramene rice genome browse page, check the "Barley1_Exemplar_GeneChip" box from "EST" menu to make it a default view option.
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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 |
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| Annotation |
1. BEST BLASTX UniProt: TBB1_WHEAT, (Q9ZRB2) Tubulin beta-1 chain (Beta-1 tubulin) Length = 445, Expect:0. match=443/445 aa. more
2. BEST BLASTX NR: Q9ZRB2, Tubulin beta-1 chain (Beta-1 tubulin) gb|AAD10487.1| beta-tubulin 1 [Triticum aestivum]
, Expect:0.
3. BEST BLASTX PLANTS: 10/14/03 1. sp|Q9ZRB2 0 TBB1_WHEAT Tubulin beta-1 chain (Beta-1 tubulin) Length = 445; 2. gb|AAD10487.1 0 beta-tubulin 1 [Triticum aestivum] Length = 445; 3. sp|Q9ZPN9 0 TBB2_ELEIN Tubulin beta-2 chain (Beta-2 tubulin) Length = 448; more
4. BEST BLASTN TIGR Barley Gene Index: TC130794, UP|TBB1_WHEAT (Q9ZRB2) Tubulin beta-1 chain (Beta-1 tubulin), complete Length = 1690, Expect: 1919, match=1665/1666. It may represent same contig. more
5. BEST TBLASTX ATH1 GeneChip Exemplar: 250317_at, ; at|At5g12250; tubulin beta-6 chain (sp|P29514) ; supported by cDNA: gi_13430695_gb_AF360260.1_AF360260 Length = 1350, Expect= 0, match=431/444 aa. more
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. |
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| Nucleotide Sequence |
Total length: 1919
>Barley1_01508
CCCAATCCCCATCCCCTCTCACTCCCCCACGCGCGACGCGAGCGCTGCAGTCCTCTCCGC
AGGGAGGCGAAGATGAGGGAGATCCTGCACATCCAGGGCGGGCAGTGCGGGAACCAGATC
GGGTCCAAGTTCTGGGAGGTGGTGTGCGACGAGCACGGCATCGACCCCACGGGGAGGTAC
GTCGGCACGTCCGACCTGCAGCTGGAGCGCGTCAACGTCTACTACAACGAGGCCTCATGC
GGCCGCTTCGTGCCGCGCGCCGTGCTCATGGATCTCGAGCCCGGCACCATGGACTCCGTC
CGCACGGGGCCGTACGGCCAGATCTTCCGCCCCGACAACTTCGTCTTCGGCCAGTCCGGC
GCCGGCAACAACTGGGCCAAGGGACACTACACCGAGGGCGCGGAGCTCATCGACTCCGTC
CTCGACGTCGTCCGCAAGGAGGCTGAGAACTGCGACTGCCTCCAAGGCTTCCAGGTGTGC
CACTCCCTGGGCGGGGGCACCGGTTCCGGCATGGGCACGCTGCTGATTTCCAAGATCAGG
GAGGAGTACCCTGACCGGATGATGCTCACCTTCTCCGTGTTCCCATCCCCCAAGGTGTCT
GACACCGTGGTCGAGCCCTACAACGCCACCCTCTCGGTTCACCAGCTGGTGGAGAACGCG
GACGAGTGCATGGTGCTGGACAACGAGGCGCTCTACGACATCTGCTTCCGCACCCTGAAG
CTGACCACACCTAGCTTTGGTGACCTGAATCATTTGATCAGTGCCACCATGAGCGGTGTC
ACCTGCTGCCTTCGCTTCCCAGGACAGCTGAACTCAGACCTCCGCAAGCTTGCAGTCAAC
CTGATCCCCTTCCCGCGCCTCCACTTCTTCATGGTGGGCTTTGCGCCGCTCACATCTCGT
GGATCGCAGATGTACCGCTCCCTCACTGTCCCAGAACTCACACAGCAAATGTGGGACTCG
AAGAACATGATGTGTGCTGCCGACCCACGCCATGGCCGCTACCTCACAGCCTCAGCCATG
TTCCGTGGCAAGATGAGCACCAAGGAGGTTGATGAGCAGATGATCAACGTGCAGAACAAG
AACTCTTCCTACTTCGTGGAGTGGATCCCGAACAATGTCAAGTCAAGCGTGTGTGACATC
CCACCACGTGGCCTCTCCATGGCGTCCACCTTCATTGGCAACTCCACCTCCATCCAGGAG
ATGTTCCGGCGTGTGAGCGAGCAGTTCACCGCCATGTTCAGGAGGAAGGCTTTCTTGCAT
TGGTACACTGGTGAGGGGATGGACGAGATGGAGTTCACTGAGGCCGAGAGTAACATGAAT
GACCTGGTCTCTGAGTACCAGCAGTACCAGGACGCCACTGCTGACGAGGAGGGCGAGTAC
GAGGAAGAGGACGAGCTGGAGCAGGAGTAAGATCGGTGACAATTGCATCTCCATTTATGT
GGTATTGTGCTTTTCGTACAACTGGAGCTTGTTTTCGTAGGGACTAGAGGGTACCATGGC
TACAAACTATGCTGCTTGTTTGTGTGTCTTGGCATGTGTTGGATTTGTACTGCGTTCGTA
TGTAGGCATGTTCACTCGATGCTATGTTTCTTTGCGTGAATTATTTTATGTGAGGTTTCA
AGCAAGTGGATTTGAAATATAAAGTAGTAGAATGCTTTCAAGTTTGAAAAAAAAAAAAAA
AAAAACTCGAGACTAGTTCTCGAAGACCGCGACAGGGCCGCGGCCCAGGAGGCCGCCGAC
GGCAAGTGACGGTGCCACGTGCTGCTGGCGTGTAGATATACGTGTGAAGGTGTAGGCGTG
CGTGGCGGGTGTACGTGTGAGGCGACGGGTGGTGTGCTGCCGCGTGTGTATGTCTCTACT
CCTCCGAGTGTGCCGAAATGGAATAAAATGGTTTTCTAATCTAAAAAAAAAAAAAAAAA
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ESTScan2.0 Prediction ( Arabidopsis model)
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ESTScan2 CDS Prediction:
Barley1_01508 588 1 1410 contig from HarvEST v. 1.03 assembly 25 [Hordeum vulgare]
XCCCAATCCCCATCCCCTCTCACTCCCCCACGCGCGACGCGAGCGCTGCAGTCCTCTCCG
CAGGGAGGCGAAGATGAGGGAGATCCTGCACATCCAGGGCGGGCAGTGCGGGAACCAGAT
CGGGTCCAAGTTCTGGGAGGTGGTGtGCGACGAGCACGGCATCGACCCCACGGGGAGGTA
CGTCGGCACGTCCGACCTGCAGCTGGAGCGCGTCAACGTCTACTACAACGAGGCCTCATG
CGGCCGCTTCGTGCCGCGCGCCGTGCTCATGGATCTCGAGCCCGGCACCATGGACTCCGT
CCGCACGGGGCCGTACGGCCAGATCTTCCGCCCCGACAACTTCGTCTTCGGCCAGTCCGG
CGCCGGCAACAACTGGGCCAAGGGACACTACACCGAGGGCGCGGAGCTCATCGACTCCGT
CCTCGACGTCGTCCGCAAGGAGGCTGAGAACTGCGACTGCCTCCAAGGCTTCCAGGTGTG
CCACTCCCTGGGCGGGGGCACCGGTTCCGGCATGGGCACGCTGCTGATTTCCAAGATCAG
GGAGGAGTACCCTGACCGGATGATGCTCACCTTCTCCGTGTTCCCATCCCCCAAGGTGTC
TGACACCGTGGTCGAGCCCTACAACGCCACCCTCTCGGTTCACCAGCTGGTGGAGAACGC
GGACGAGTGCATGGTGCTGGACAACGAGGCGCTCTACGACATCTGCTTCCGCACCCTGAA
GCTGACCACACCTAGCTTTGGTGACCTGAATCATTTGATCAGTGCCACCATGAGCGGTGT
CACCTGCTGCCTTCGCTTCCCAGGACAGCTGAACTCAGACCTCCGCAAGCTTGCAGTCAA
CCTGATCCCCTTCCCGCGCCTCCACTTCTTCATGGTGGGCTTTGCGCCGCTCACATCTCG
TGGATCGCAGATGTACCGCTCCCTCACTGTCCCAGAACTCACACAGCAAATGTGGGACTC
GAAGAACATGATGTGTGCTGCCGACCCACGCCATGGCCGCTACCTCACAGCCTCAGCCAT
GTTCCGTGGCAAGATGAGCACCAAGGAGGTTGATGAGCAGATGATCAACGTGCAGAACAA
GAACTCTTCCTACTTCGTGGAGTGGATCCCGAACAATGTCAAGTCAAGCGTGTGTGACAT
CCCACCACGTGGCCTCTCCATGGCGTCCACCTTCATTGGCAACTCCACCTCCATCCAGGA
GATGTTCCGGCGTGTGAGCGAGCAGTTCACCGCCATGTTCAGGAGGAAGGCTTTCTTGCA
TTGGTACACTGGTGAGGGGATGGACGAGATGGAGTTCACTGAGGCCGAGAGTAACATGAA
TGACCTGGTCTCTGAGTACCAGCAGTACCAGGACGCCACTGCTGACGAGGAGGGCGAGTA
CGAGGAAGAGGACGAGCTGGAGCAGGAGTAA
Protein Prediction:
QSPSPLTPPRATRALQSSPQGGEDEGDPAHPGRAVREPDRVQVLGGGGDEHGIDPTGRYV
GTSDLQLERVNVYYNEASCGRFVPRAVLMDLEPGTMDSVRTGPYGQIFRPDNFVFGQSGA
GNNWAKGHYTEGAELIDSVLDVVRKEAENCDCLQGFQVCHSLGGGTGSGMGTLLISKIRE
EYPDRMMLTFSVFPSPKVSDTVVEPYNATLSVHQLVENADECMVLDNEALYDICFRTLKL
TTPSFGDLNHLISATMSGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMVGFAPLTSRG
SQMYRSLTVPELTQQMWDSKNMMCAADPRHGRYLTASAMFRGKMSTKEVDEQMINVQNKN
SSYFVEWIPNNVKSSVCDIPPRGLSMASTFIGNSTSIQEMFRRVSEQFTAMFRRKAFLHW
YTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEEGEYEEEDELEQE
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