Barley1 GeneChip Exemplar: Barley1_05907
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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_05907:
1. Contig5907_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: Q8W5R9, BZIP transcription factor Length = 334, Expect:0. match=291/307 aa. more
2. BEST BLASTX NR: BAB72062.1, bZIP transcription factor [Oryza sativa] dbj|BAC79596.1| bZIP transcription factor [Oryza sativa (japonica cultivar-group)]
, Expect:1e-160.
3. BEST BLASTX PLANTS: 10/14/03 1. dbj|BAC79596.1 0 bZIP transcription factor [Oryza sativa (japonica cultivar-group)] Length = 334; 2. dbj|BAB72062.1 0 bZIP transcription factor [Oryza sativa] Length = 334; 3. dbj|BAB72061.1 0 bZIP transcription factor [ more
4. BEST BLASTN TIGR Barley Gene Index: TC133630, homologue to UP|Q7X993 (Q7X993) BZIP transcription factor, complete Length = 1796, Expect: 1308, match=1291/1291. It may represent same contig. more
5. BEST TBLASTX ATH1 GeneChip Exemplar: 250671_at, ; at|At5g06950; transcription factor HBP-1b homolog (sp|P43273) ; supported by cDNA: gi_217826_dbj_D10042.1_ATHAHBP1B Length = 993, Expect= 0, match=167/232 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: 1308
>Barley1_05907
GGTGGTGGGGCAATCATGGCTTCTAATTCTTCGGATAGGTCTGACAGGTCCGACAAACCC
TTGGACCAAAAGACATTGCGTCGTCTTGCTCAAAATCGTGAGGCTGCAAGGAAAAGTCGA
CTAAGGAAGAAGTCATATGTGCAACAGCTAGAAAGCAGCAAGCTGAAGCTTGCACAACTA
GAGCAGGAGCTCCAGAAAGCTCGCCAGCAGGGAATCTTCATTTCTAGCTCCGGAGACCAA
ACCCATGCCATGAGTGGAAACGGAGCAATGACTTTCGACCTAGAATACACTAGATGGCTT
GAGGACCAAAACAAGCAAATCAATGAGTTGAGGACTGCAGTTAATGCTCATGCAAGTGAC
AGTGACCTGCGCCTTATCGTAGATGGGATAATGTCACATTATGATGAGATATTTAAGGTC
AAAGGTGTAGCTGCCAAGGCTGACGTGTTCCATATACTGTCAGGCATGTGGAAAACGCCT
GCTGAAAGGTGCTTCCTATGGCTTGGGGGTTTCCGTCCATCCGAGCTCTTAAAGCTGCTG
GTGAATCATCTGGAGCCGCTAACCGAGCAGCAGATGTTGGGATTGACCAACCTCCAGCAA
TCTTCCCAGCAGGCAGAGGATGCACTGTCACAAGGGATGGAAGCATTGCAGCAATCACTG
GCAGAGACTTTGGCTGGATCTCTGGGTTCCTCCTCTGGTTCTTCAGGGAATGTTGCAAAC
TACATGGGTCAGATGGCCATGGCCATGGGCAAGCTTGGAACACTCGAGAACTTTCTTCGC
CAGGCTGACAACCTGCGACAGCAGACCTTGCATCAAATGCAGCGAATCTTGACGATCCGT
CAGGCCTCCCGTGCCCTTCTAGCTATACATGACTACTTCTCGCGTTTGCGCGCGCTGAGC
TCTCTGTGGCTTGCTAGGCCCAGGGAATAACCAAGGATCGCTCGCTCGCCGGATTTCCCC
CAAGCTGATCTGTACAACGCTGGGGGCTCTCTTCATATTGCTGCAGATAATTTGGGTATT
CGAGTTTTTCTTTCTTGTATAATTATGTGTAGCTGCTTTTTGGGTCCAGGGTTTGTTGTA
CTCGGGTGGTATACAAGTAGGTGGGGGGAGCCTGTAAGTTACAATGGTTGTAGAACTGTG
TTGGGAATAAAAACTAGATAAGTCAGGACGGGTCCTAATTAAGTCGTGTCTCGGTACTGT
AGTGGCTGGAAAATCGGTGCTCCGTGTATTTTAGCTGTTGACTGTTGTCCCTGTGGTGGT
TGAACATGGTGAATACATATGAACTTGTTCCAAAAAAAAAAAAAAAAA
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ESTScan2.0 Prediction ( Arabidopsis model)
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ESTScan2 CDS Prediction:
Barley1_05907 699 1 917 contig from HarvEST v. 1.03 assembly 25 [Hordeum vulgare]
GGTGGTGGGGCAATCATGGCTTCTAATTCTTCGGATAGGTCTGACAGGTCCGACAAACCC
TTGGACCAAAAGACATTGCGTCGTCTTGCTCAAAATCGTGAGGCTGCAAGGAAAAGTCGA
CTAAGGAAGAAGTCATATGTGCAACAGCTAGAAAGCAGCAAGCTGAAGCTTGCACAACTA
GAGCAGGAGCTCCAGAAAGCTCGCCAGCAGGGAATCTTCATTTCTAGCTCCGGAGACCAA
ACCCATGCCATGAGTGGAAACGGAGCAATGACTTTCGACCTAGAATACACTAGATGGCTT
GAGGACCAAAACAAGCAAATCAATGAGTTGAGGACTGCAGTTAATGCTCATGCAAGTGAC
AGTGACCTGCGCCTTATCGTAGATGGGATAATGTCACATTATGATGAGATATTTAAGGTC
AAAGGTGTAGCTGCCAAGGCTGACGTGTTCCATATACTGTCAGGCATGTGGAAAACGCCT
GCTGAXAAGGTGCTTCCTATGGCTTGGGGGTTTCCGTCCATCCGAGCTCTTAAAGCTGCT
GGTGAATCATCTGGAGCCGCTAACCGAGCAGCAGATGTTGGGATTGACCAACCTCCAGCA
ATCTTCCCAGCAgGCAGAGGATGCACTGTCACAAGGGATGGAAGCATTGCAGCAATCACT
GGCAGAGACTTTGGCTGGATCTCTGGGTTCCTCCTCTGGTTCTTCAGGGAATGTTGCAAA
CTACATGGGTCAGATGGCCATGGCCATGGGCAAGCTTGGAACACTCGAGAACTTTCTTCG
CCAGGCTGACAACCTGCGACAGCAGACCTTGCATCAAATGCAGCGAATCTTGACGATCCG
TCAGGCCTCCCGTGCCCTTCTAGCTATACATGACTACTTCTCGCGTTTGCGCGXCGCTGA
GCTCTCTGTGGCTTGCTAG
Protein Prediction:
GGGAIMASNSSDRSDRSDKPLDQKTLRRLAQNREAARKSRLRKKSYVQQLESSKLKLAQL
EQELQKARQQGIFISSSGDQTHAMSGNGAMTFDLEYTRWLEDQNKQINELRTAVNAHASD
SDLRLIVDGIMSHYDEIFKVKGVAAKADVFHILSGMWKTPAXKVLPMAWGFPSIRALKAA
GESSGAANRAADVGIDQPPAIFPAAEDALSQGMEALQQSLAETLAGSLGSSSGSSGNVAN
YMGQMAMAMGKLGTLENFLRQADNLRQQTLHQMQRILTIRQASRALLAIHDYFSRLRXAE
LSVAC
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