Barley1 GeneChip Exemplar: Barley1_49972
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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_49972:
1. rbags23g22_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: O24564, Embryogenesis transmembrane protein Length = 1389, Expect:4e-36. match=76/146 aa. more
2. BEST BLASTX NR: T03273, embryogenesis transmembrane protein - maize emb|CAA66183.1| embryogenesis transmembrane protein [Zea mays]
, Expect:3e-21.
3. BEST BLASTX PLANTS: 10/14/03 1. emb|CAA66183.1 1e-036 embryogenesis transmembrane protein [Zea mays] Length = 1389; 2. T03273 1e-036 pir|| embryogenesis transmembrane protein - maize Length = 1389; more
4. BEST BLASTN TIGR Barley Gene Index: AV921439, weakly similar to PIR|T03273|T03 embryogenesis transmembrane protein - maize, partial (4%) Length = 629, Expect:656, match=620/622. 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. |
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| Nucleotide Sequence |
Total length: 656
>Barley1_49972
GAGAACAGAGCACAAATGGCGCAAAGATTTGATGCTGATTGGAACTCTTGCAGTCACTGT
CACATACCAAGCTGGTCTGCTTCCGCCTGGAGGAGTTTGGCCTGATGACAAGGATGGCCA
TTTTGCAGGTGACCCAATCCTCCATGATACCAACCTAACACGATACAAGGTATTCTTCTA
TTGCAACGCCACAGCATTCATGGCCTCAATGGTAATGGTCATCCTCCTACTGAACAACAC
AATAAGCAAGTACAAGAGATCTCTCTTTGCCATGAAAACAGCAATGGTATTGGACTTGCT
TGGTTTACTTGGGGCATATGCCGCGGGCAGCTGCAGGAAGTTGAAGACATCTGTGTACAT
TTTTGCACTCGTCATTGCTGTGATCATCTACATCGTCATCCATGTCTTGTTGTCATTTGA
CGAATTGGGAAGCTTAGTGAAGGAGAAGGGGAAAAAGTGGGTGCAACGTTTGAAAAGGTT
CTTCAATTGCAACGATTCAAGCAATGAACCATCTGATGGGGAACCAGGACAAAGTCGTCT
GCCTGTGAAAGAGATAGTCTCGGTTGTGACATTTGTTGAGTCTATCATGAGATAGACACA
ACCTCCAAAGTTGTAATTTGTGTTTTTACGTGCTCAAGCGCCGTCACCGTAATATT
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ESTScan2.0 Prediction ( Arabidopsis model)
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ESTScan2 CDS Prediction:
Barley1_49972 512 1 595 contig from HarvEST v. 1.03 assembly 25 [Hordeum vulgare]; minus strand
XXGAGAACAGAGCACAAATGGCGCAAAGATTTGATGCTGATTGGAACTCTTGCAGTCACT
GTCACATACCAAGCTGGTCTGCTTCCGCCTGGAGGAGTTTGGCCTGATGACAAGGATGGC
CATTTTGCAGGTGACCCAATCCTCCATGATACCAACCTAACACGATACAAGGTATTCTTC
TATTGCAACGCCACAGCATTCATGGCCTCAATGGTAATGGTCATCCTCCTACTGAACAAC
ACAATAAGCAAGTACAAGAGATCTCTCTTTGCCATGAAAACAGCAATGGTATTGGACTTG
CTTGGTTTACTTGGGGCATATGCCGCGGGCAGCTGCAGGAAGTTGAAGACATCTGTGTAC
ATTTTTGCACTCGTCATTGCTGTGATCATCTACATCGTCATCCATGTCTTGTTGTCATTT
GACGAATTGGGAAGCTTAGTGAAGGAGAAGGGGAAAAAGTGGGTGCAACGTTTGAAAAGG
TTCTTCAATTGCAACGATTCAAGCAATGAACCATCTGATGGGGAACCAGGACAAAGTCGT
CTGCCTGTGAAAGAGATAGTCTCGGTTGTGACATTTGTTGAGTCTATCATGAGATAG
Protein Prediction:
RTEHKWRKDLMLIGTLAVTVTYQAGLLPPGGVWPDDKDGHFAGDPILHDTNLTRYKVFFY
CNATAFMASMVMVILLLNNTISKYKRSLFAMKTAMVLDLLGLLGAYAAGSCRKLKTSVYI
FALVIAVIIYIVIHVLLSFDELGSLVKEKGKKWVQRLKRFFNCNDSSNEPSDGEPGQSRL
PVKEIVSVVTFVESIMR
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