Barley1 GeneChip Exemplar: Barley1_11969
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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_11969:
1. Contig11969_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: Q8GZY1, Hypothetical protein OSJNBa0090O10.1 Length = 519, Expect:0. match=211/312 aa. more
2. BEST BLASTX NR: AAD48912.1, aldehyde 5-hydroxylase [Liquidambar styraciflua]
, Expect:1e-110.
3. BEST BLASTX PLANTS: 10/14/03 1. emb|CAC40582.1 0 unnamed protein product [Zea mays] Length = 526; 2. emb|CAC40581.1 0 unnamed protein product [Zea mays] Length = 532; 3. gb|AAO17011.1 0 Hypothetical protein [Oryza sativa (japonica cultivar-group)] Leng more
4. BEST BLASTN TIGR Barley Gene Index: BM371202, Length = 647, Expect:1161, match=647/647. It may represent same contig. more
5. BEST TBLASTX ATH1 GeneChip Exemplar: 253088_at, ; at|At4g36220; ferulate-5-hydroxylase (FAH1) ; supported by cDNA: gi_1488254_gb_U38416.1_ATU38416 Length = 1563, Expect= 0, match=101/164 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: 1161
>Barley1_11969
GCAGGAGTTCTCCCATCTCTTCGCCGCGTTCAGCCTCGGCGACTTCATCCCGTGGCTCAG
CTGGGCGGACCAGGGCACCAACGTGCGCGCCCGCGCTGCGCGCGCCGCCCTCGACGAGTT
CATCGATTTTATCATCGACGAGCACGTGGAGAGAGGTAAGAACCCCGACGACGTGGACGC
CGACATGGTGGACGACATGCTCGCGTTCCTGTCTGAGGCGAAGCCGAAGGAGGCCGATGG
CGACGACCTGCAGAACACGCTCCGCCTCACCCGTGACAACATCAAAGCCATGATCATGGA
CGTGATGTTTGGTGGGACGGAGACGGTGGCATCCGGGATTGAGTGGGCAATGGCAGAGAT
GATGCAAAGCCCCAACGAGCTTCGTCGGCTGCAGGAGGAGCTTGCTGACGTGGTGGGCCT
CGACCGAAATGTAGATGAGTCGGACCTCGACAAGCTCCCCTTCCTCAAGTGCGTAATCAA
GGAGACGCTTCGACTACACCCGCCCATCCCGATTCTCCACCACGAGAACGCTAAGGATTG
TGTGGTCGGTGGCTATTCAGTACCCCAGGGCTCAAGTATCATGATCAACGTCTTCGACAT
TGGTCGAAACGCCAAGGTGTGGAAGGACGCCGACATGTTCCGACCGTCGAGGTTTATGGC
AGTGGAAGGAGAGGCCGCAAAGGTGGATTTCAAGGGCAACTGCTTCGAGTTCCTGCCGTT
CGGGTCTGGCCGCCGCTCGTGCCCTGGGATGGCGCTTGGCATCTACTCACTGGAATTTGC
TGTCGCCCAACTCGCCCACGGGTTCAACTGGGCGCTGCCCGATGGCATGAAGCCGTCGGA
GCTCGACATGACCGACATCTTCGGACTCACCGCGCCGCGCGCCAGCAGGCTCTGCGCCGT
GCCAACGCCCCGGCTTTCGCACCCTTGGGTCTCCGACGTTGATGCCACGCACAAGGCGTG
ATGTCGTGTTGTATGCGCACGGGAAAGTACATTCATCCTGTGACACAATAAAGATGTTTC
ACCCGGTTCAGGATGACACAATATCAGCGTATTAGACAACGGGTCCATTCGTCCATGGAT
CCAAAATTTAATCAAACTTTGTACACAATTGACCAAGTTTATGGATACTTTTAGATCCTG
CATTAAAAAAAAAAAAAAAAA
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ESTScan2.0 Prediction ( Arabidopsis model)
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ESTScan2 CDS Prediction:
Barley1_11969 303 1 1055 contig from HarvEST v. 1.03 assembly 25 [Hordeum vulgare]; minus strand
GCAGGAGTTCTCCCATCTCTTCGCCGCGTTCAGCCTCGGCGACTTCATCCCGTGGCTCAG
CTGGGCGGACCAGGGCACCAACGTGCGCGCCCGCGCTGCGCgCGCCGCCCTCGACGAGTT
CATCGATTTTATCATCGACGAGCACGTGGAGAGAGGTAAGAACCCCGACGACGTGGACGC
CGACATGGTGGACGACATGCTCGCGTTCCTGTCTGAGGCGAAGCCGAAGGAGGCCGATGG
CGACGACCTGCAGAACACGCTCCGCCTCACCCGTGACAACATCAAAGCCATGATCATGGA
CGTGATGTTTGGTGGGACGGAGACGGTGGCATCCGGGATTGAGTGGGCAATGGCAGAGAT
GATGCAAAGCCCCAACGAGCTTCGTCGGCTGCAGGAGGAGCTTGCTGACGTGGTGGGCCT
CGACCGAAATGTAGATGAGTCGGACCTCGACAAGCTCCCCTTCCTCAAGTGCGTAATCAA
GGAGACGCTTCGACTACACCCGCCCATCCCGATTCTCCACCACGAGAACGCTAAGGATTG
TGTGGTCGGTGGCTATTCAGTACCCCAGGGCTCAAGTATCATGATCAACGTCTTCGACAT
TGGTCGAAACGCCAAGGTGTGGAAGGACGCCGACATGTTCCGACCGTCGAGGTTTATGGC
AGTGGAAGGAGAGGCCGCAAAGGTGGATTTCAAGGGCAACTGCTTCGAGTTCCTGCCGTT
CGGGTCTGGCCGCCGCTCGTGCCCTGGGATGGCGCTTGGCATCTACTCACTGGAATTTGC
TGTCGCCCAACTCGCCCACGGGTTCAACTGGGCGCTGCCCGATGGCATGAAGCCGTCGGA
GCTCGACATGACCGACATCTTCGGACTCACCGCGCCGCgCGCCAGCAGGCTCTGCGCCGT
GCCAACGCCCCGGCTTTCGCACCCTTGGGTCTCCGACGTTGATGCCACGCACAAGGCGTG
ATGTCGTGTTGTATGCGCACGGGAAAGTACATTCATCCTGTGACACAATAAAGATGTTTC
ACCCGGTTCAGGATGACACAATATCAGCGTATTAG
Protein Prediction:
AGVLPSLRRVQPRRLHPVAQLGGPGHQRARPRCAAALDEFIDFIIDEHVERGKNPDDVDA
DMVDDMLAFLSEAKPKEADGDDLQNTLRLTRDNIKAMIMDVMFGGTETVASGIEWAMAEM
MQSPNELRRLQEELADVVGLDRNVDESDLDKLPFLKCVIKETLRLHPPIPILHHENAKDC
VVGGYSVPQGSSIMINVFDIGRNAKVWKDADMFRPSRFMAVEGEAAKVDFKGNCFEFLPF
GSGRRSCPGMALGIYSLEFAVAQLAHGFNWALPDGMKPSELDMTDIFGLTAPPPAGSAPC
QRPGFRTLGSPTLMPRTRRDVVLYAHGKVHSSCDTIKMFHPVQDDTISAY
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