Barley1 GeneChip Exemplar: Barley1_03144
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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_03144:
1. Contig3144_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: APR1_ORYSA, (Q42456) Aspartic proteinase oryzasin 1 precursor (EC 3.4.23.-) Length = 509, Expect:0. match=335/508 aa. more
2. BEST BLASTX NR: Q42456, Aspartic proteinase oryzasin 1 precursor pir||S66516 oryzasin (EC 3.4.23.-) precursor - rice
, Expect:0.
3. BEST BLASTX PLANTS: 10/14/03 1. S66516 0 pir|| oryzasin (EC 3.4.23.-) precursor - rice Length = 509; 2. sp|P42210 0 ASPR_HORVU Phytepsin precursor (Aspartic proteinase) Length = 508; 3. dbj|BAA06875.1 0 aspartic protease [Oryza sativa] Length = 509; more
4. BEST BLASTN TIGR Barley Gene Index: TC131356, similar to PDB|1QDM_A.0|5822248|1QDM_A Chain A, Crystal Structure Of Prophytepsin, A Zymogen Of A Barley Vacuolar Aspartic Proteinase. {Hordeum vulgare;} , partial (91%) Length = 1704, Expect: 1717, match=1698/1698. It may represent same contig. more
5. BEST TBLASTX ATH1 GeneChip Exemplar: 264344_at, ; at|At1g11910; putative aspartic proteinase similar to GB:AAC49730;supported by full-length cDNA: Ceres:8972. Length = 1521, Expect= 0, match=198/311 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: 1717
>Barley1_03144
GGACACCACCGATCCTGGTTGGCAACCATGGCAGCCGCTGGCCACCTCATCCTCCTGTCA
TGCGTGCTCCTTCACGCCCTCCTCGCCGGTCCGGCGGAGGGTCTGGTCCGTGTCGCGCTG
ACGAAGCGGCCGGCGGACGAGGACGGACGCGTCGTCGCCGGGGAGGACGCGCAGCGCCTC
CTCGCGTGGCGGCACGGCCTCGTCTACAACTCCGCCGCCCACGTGCCCAAAGAAGGCGCG
GAGGGCCACGTCGTGGCGCTTAAGAACCACCTCAACGCCCAGTACTACGGTGAGATCGCC
ATCGGGACGCCGCCGCAGAACTTCACCGTCATCTTCGACACGGGCAGCGCCGAGTTCTGG
GTGCCCTCCTCCAAGTGCTTTCTCTCGATTGCATGCTACCTCCATGCGAGCTACAAGGCC
AGCAAGTCCACCACTTACAAGAAGAACGGAAAAAGGGTTGCACTTCATTATGGAACCGGT
ACAATTTCTGGATATATTAGCCAGGACAATGTCCAAGTTGGTGGCCTAGTTGTAAAAAAT
CAGGATTTCATCGAAGCTACCTTGGAACCGGGTATAACTTTCATGTTTAGGAAATTCGAT
GGCATTCTCGGTCTTGGGTTTAAAGAAATCGCAAAAGGCAATGTTGAACCTGTCTGGTAC
AACATGGTTAATCAACATCTGGTTGGTAGCCCCATTTTCTCATTCTGGTTCAACCGACAT
GCCGACAATGGGCAGGGGGGAGAAATTGTGTTTGGAGGAATTGATCCTAAGCATCACAAG
GAAGAGCATAAATACGTTCCTATTACTAAGAAGGGATACTGGCAGTTTGATATGGGTGAT
GTCTTGATTGGAGGAAACTCCACAGGATTATGTGCATCTCGATGTGCAGCTATAGCAGAT
TCGGGAACTTCGTTGCTTGTTGGCCCCACAGCCATAATTGCTCAGATAAATGAAAAGATT
GGTGCGCCTGGAATTCTCAGCCAAGAGTGCAAGGCAGTTGCTTCTCAGTATGGGCAACGG
ATCTTACAACTGATGCTAGATGGGATCGACCCGACAAAAATATGTCCTTCTATTGGTCTA
TGCATTCAGAATGGAACTCAAGGTGTGAGCTTTGGTATTCGGAATGTGGTAGATGATGAA
GCTGGGAGATCAAATGATGCCATGTGCCATGTTTGTGAGATGGCTGTTATGTGGGCAAAG
AACCAACTTGCACAGGATCGAACACGGGATCTTATATTGAAGTACATTAATAAGCTATGT
GACTATATCCCTAGCCCTATGGGAGAATCATCAGTGGACTGCAAAAGACTTGAATCCCTG
CCCGACGTCGCCTTCACCATCGGCGGCAAACAGTTTGCCCTCAAACCAGAGGAATACATC
CTGAAGGTCGGTGACGGAGATGCTACTCAGTGCATTAGTGGATTCATAGCCATGGATATT
CCTCCCCCAAATGGTCCTATCTGGATCTTGGGCGACATATTCATGGGAGCCTATCACACT
GTCTTCGACTATGGTAACATGAAGGTTGGCTTTGCGAAGGCGGCATAGGTAACCAGACGA
GCCGCAAAGGATTTGTCTTTCATGACATTTTCTTATAGATGTTTCATAATTCCCGTGTGG
TTTAAGATAATAAACATGTATGTGTTTCAAATTGGCCAAGATACAGTCATAATTCAATAT
GGGAAGGATTAATATTTAAAAAAAAAAAAAAAAAAAA
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ESTScan2.0 Prediction ( Arabidopsis model)
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ESTScan2 CDS Prediction:
Barley1_03144 921 1 1548 contig from HarvEST v. 1.03 assembly 25 [Hordeum vulgare]
XXGGACACCACCGATCCTGGTTGGCAACCATGGCAGCCGcTGGCCACCTCATCCTCCTGT
CATGCGTGCTCCTTCACGCCCTCCTCGCCGGTCCGGCGGAGGGTCTGGTCCGTGTCGCGC
TGACGAAGCGGcCGGCGGACGAGGACGGACGCGTCGTCGCCGGGGAGGACGCGCAGCGCC
TCCTCGCGTGGCGGCACGGCCTCGTCTACAACTCCGCCGCCCACGTGCCCAAAGAAGGCG
CGGAGGGCCACGTCGTGGCGCTTAAGAACCACCTCAACGCCCAGTACTACGGTGAGATCG
CCATCGGGACGCCGCCGCAGAACTTCACCGTCATCTTCGACACGGGCAGCGCCGAGTTCT
GGGTGCCCTCCTCCAAGTGCTTTCTCTCGATTGCATGCTACCTCCATGCGAGCTACAAGG
CCAGCAAGTCCACCACTTACAAGAAGAACGGAAAAAGGGTTGCACTTCATTATGGAACCG
GTACAATTTCTGGATATATTAGCCAGGACAATGTCCAAGTTGGTGGCCTAGTTGTAAAAA
ATCAGGATTTCATCGAAGCTACCTTGGAACCGGGTATAACTTTCATGTTTAGGAAATTCG
ATGGCATTCTCGGTCTTGGGTTTAAAGAAATCGCAAAAGGCAATGTTGAACCTGTCTGGT
ACAACATGGTTAATCAACATCTGGTTGGTAGCCCCATTTTCTCATTCTGGTTCAACCGAC
ATGCCGACAATGGGCAGGGGGGAGAAATTGTGTTTGGAGGAATTGATCCTAAGCATCACA
AGGAAGAGCATAAATACGTTCCTATTACTAAGAAGGGATACTGGCAGTTTGATATGGGTG
ATGTCTTGATTGGAGGAAACTCCACAGGATTATGTGCATCTCGATGTGCAGCTATAGCAG
ATTCGGGAACTTCGTTGCTTGTTGGCCCCACAGCCATAATTGCTCAGATAAATGAAAAGA
TTGGTGCGCCTGGAATTCTCAGCCAAGAGTGCAAGGCAGTTGCTTCTCAGTATGGGCAAC
GGATCTTACAACTGATGCTAGATGGGATCGACCCGACAAAAATATGTCCTTCTATTGGTC
TATGCATTCAGAATGGAACTCAAGGTGTGAGCTTTGGTATTCGGAATGTGGTAGATGATG
AAGCTGGGAGATCAAATGATGCCATGTGCCATGTTTGTGAGATGGCTGTTATGTGGGCAA
AGAACCAACTTGCACAGGATCGAACACGGGATCTTATATTGAAGTACATTAATAAGCTAT
GTGACTATATCCCTAGCCCTATGGGAGAATCATCAGTGGACTGCAAAAGACTTGAATCCC
TGCCCGACGTCGCCTTCACCATCGGCGGCAAACAGTTTGCCCTCAAACCAGAGGAATACA
TCCTGAAGGTCGGTGACGGAGATGCTACTCAGTGCATTAGTGGATTCATAGCCATGGATA
TTCCTCCCCCAAATGGTCCTATCTGGATCTTGGGCGACATATTCATGGGAGCCTATCACA
CTGTCTTCGACTATGGTAACATGAAGGTTGGCTTTGCGAAGGCGGCATAG
Protein Prediction:
DTTDPGWQPWQPWPPHPPVMRAPSRPPRRSGGGSGPCRADEAAADEDGRVVAGEDAQRLL
AWRHGLVYNSAAHVPKEGAEGHVVALKNHLNAQYYGEIAIGTPPQNFTVIFDTGSAEFWV
PSSKCFLSIACYLHASYKASKSTTYKKNGKRVALHYGTGTISGYISQDNVQVGGLVVKNQ
DFIEATLEPGITFMFRKFDGILGLGFKEIAKGNVEPVWYNMVNQHLVGSPIFSFWFNRHA
DNGQGGEIVFGGIDPKHHKEEHKYVPITKKGYWQFDMGDVLIGGNSTGLCASRCAAIADS
GTSLLVGPTAIIAQINEKIGAPGILSQECKAVASQYGQRILQLMLDGIDPTKICPSIGLC
IQNGTQGVSFGIRNVVDDEAGRSNDAMCHVCEMAVMWAKNQLAQDRTRDLILKYINKLCD
YIPSPMGESSVDCKRLESLPDVAFTIGGKQFALKPEEYILKVGDGDATQCISGFIAMDIP
PPNGPIWILGDIFMGAYHTVFDYGNMKVGFAKAA
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