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OryzaPG-DB:: The Rice Proteogenomics Database

Proteogenomics (PG) is a recent research trend aiming to utilize the proteome information in the discovery of new genomic features in both eukaryotic and prokaryotic organisms. The proteome information is an incomparable source of translation evidence of the genes. While, the MS/MS based proteomics provides high-throughput peptides-based proteome data. Thus, the MS/MS based peptides-based proteomics became the technology-of-choice for many proteogenomics projects. The information are provides in three fl...

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OryzaPG-DB:: The Rice Proteogenomics Database | oryzapg.iab.keio.ac.jp Reviews

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Proteogenomics (PG) is a recent research trend aiming to utilize the proteome information in the discovery of new genomic features in both eukaryotic and prokaryotic organisms. The proteome information is an incomparable source of translation evidence of the genes. While, the MS/MS based proteomics provides high-throughput peptides-based proteome data. Thus, the MS/MS based peptides-based proteomics became the technology-of-choice for many proteogenomics projects. The information are provides in three fl...

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6 genes

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OryzaPG-DB:: The Rice Proteogenomics Database | oryzapg.iab.keio.ac.jp Reviews

https://oryzapg.iab.keio.ac.jp

Proteogenomics (PG) is a recent research trend aiming to utilize the proteome information in the discovery of new genomic features in both eukaryotic and prokaryotic organisms. The proteome information is an incomparable source of translation evidence of the genes. While, the MS/MS based proteomics provides high-throughput peptides-based proteome data. Thus, the MS/MS based peptides-based proteomics became the technology-of-choice for many proteogenomics projects. The information are provides in three fl...

INTERNAL PAGES

oryzapg.iab.keio.ac.jp

1

OryzaPG-DB:: The Rice Proteogenomics Database

http://oryzapg.iab.keio.ac.jp/sample_genes.php?chr=0&sid=1

8226;• DATABASE SEARCH. 8226;• DATABASE STATISTICS. The Database Currently Contains:. Genes to Be Revised:. Browsing genes of all chromosomes and Cultured cells proteome sample. Save data to file. MSU/TIGR (V6.1) Locus:. Protein acetyl-CoA acetyltransferase, cytosolic, putative, expressed. Novel Peptides and Genomic Features ( 0. 1- From Protein DB:. 2- From cDNA DB:. 2- Acceptor Spanning Peptides:. 3- From Gene DB:. 3- Donor Spanning Peptides:. 4- From Genome DB:. Gene Model Details: Protein Products.

2

OryzaPG-DB:: The Rice Proteogenomics Database

http://oryzapg.iab.keio.ac.jp/all_genes.php?chr=1

8226;• DATABASE SEARCH. 8226;• DATABASE STATISTICS. The Database Currently Contains:. Genes to Be Revised:. Browsing genes on Chromosome #1. Save data to file. MSU/TIGR (V6.1) Locus:. Protein RNA recognition motif, putative, expressed. Novel Peptides and Genomic Features ( 0. 1- From Protein DB:. 2- From cDNA DB:. 2- Acceptor Spanning Peptides:. 3- From Gene DB:. 3- Donor Spanning Peptides:. 4- From Genome DB:. Gene Model Details: Protein Products. Updated Annotation (.gff3). MSU/TIGR (V6.1) Locus:.

3

OryzaPG-DB:: The Rice Proteogenomics Database

http://oryzapg.iab.keio.ac.jp/cdnas.php?chr=1

8226;• DATABASE SEARCH. 8226;• DATABASE STATISTICS. The Database Currently Contains:. Genes to Be Revised:. Browsing cDNA(s) on chromosome Chromosome #1. Save data to file. MSU/TIGR (V6.1) Locus:. CDNA 40S ribosomal protein S5, putative, expressed. MSU/TIGR (V6.1) Locus:. CDNA decarboxylase, putative, expressed. MSU/TIGR (V6.1) Locus:. CDNA decarboxylase, putative, expressed. MSU/TIGR (V6.1) Locus:. CDNA decarboxylase, putative, expressed. MSU/TIGR (V6.1) Locus:. MSU/TIGR (V6.1) Locus:. MSU/TIGR (V6....

4

OryzaPG-DB:: The Rice Proteogenomics Database

http://oryzapg.iab.keio.ac.jp/publications.php

Jan-30-2012) OryzaPG-DB content updated. The contents of OryzaPG-DB was updated to OryzaPG-DB v1.1 by adding the rice phosphoproteome data obtained from 34 LC-MS/MS runs of rice undifferentiated cultured cell. Please note that, the files in the downloads page are for OryzaPG-DB and will be updated soon. May-14-2011) OryzaPG-DB article marked Highly accessed by BMC Plant Biology. April-12-2011) OryzaPG-DB published at BMC Plant Biology. 2011, 11:63, doi:10.1186/1471-2229-11-63. The Rice proteogenomics Dat...

5

OryzaPG-DB:: The Rice Proteogenomics Database

http://oryzapg.iab.keio.ac.jp/downloads.php

1- Original MSU/TIGR (V6.1) genome annotation. The rar file includes 12 file, file per chromosome, contains the original genome annotation obtained from MSU/TIGR (V6.1) genome browser. The selected features are MSU Osa1 Rice Gene Models and MSU Osa1 Rice Loci. The annotation is in .gff3 format. 2- The MSU/TIGR (V6.1) protein databse. The protein database and FASTA sequence were obtained from MSU/TIGR (V6.1) database. 3- The MSU/TIGR (V6.1) cDNA databse. 4- The MSU/TIGR (V6.1) transcript databse.

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OryzaPG-DB:: The Rice Proteogenomics Database

Proteogenomics (PG) is a recent research trend aiming to utilize the proteome information in the discovery of new genomic features in both eukaryotic and prokaryotic organisms. The proteome information is an incomparable source of translation evidence of the genes. While, the MS/MS based proteomics provides high-throughput peptides-based proteome data. Thus, the MS/MS based peptides-based proteomics became the technology-of-choice for many proteogenomics projects. The information are provides in three fl...

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