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Proteomes - Oryza sativa subsp. japonica (Rice)

Overview

Proteinsi <p>Number of protein entries associated with this proteome: UniProtKB entries for regular proteomes or UniParc entries for redundant proteomes (<a href="/help/proteome%5Fredundancy">more...</a>)</p> 59,202
Gene counti <p>This is the total number of unique genes found in the proteome set, algorithmically computed. For each gene, a single representative protein sequence is chosen from the proteome. Where possible, reviewed (Swiss-Prot) protein sequences are chosen as the representatives.</p> - Download one protein sequence per gene (FASTA)
Proteome IDi <p>The proteome identifier (UPID) is the unique identifier assigned to the set of proteins that constitute the <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a>. It consists of the characters 'UP' followed by 9 digits, is stable across releases and can therefore be used to cite a UniProt proteome.<p><a href='/help/proteome_id' target='_top'>More...</a></p>UP000000763
Taxonomy39947 - Oryza sativa subsp. japonica
Straincv. Nipponbare
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000005425.2 from ENA/EMBL full
Buscoi <p>The Benchmarking Universal Single-Copy Ortholog (BUSCO) assessment tool is used, for eukaryotic and bacterial proteomes, to provide quantitative measures of UniProt proteome data completeness in terms of expected gene content. BUSCO scores include percentages of complete (C) single-copy (S) genes, complete (C) duplicated (D) genes, fragmented (F) and missing (M) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment, and the name of the taxonomic lineage dataset used.</p> C:89.9%[S:25.2%,D:64.7%],F:3.7%,M:6.5%,n:4896 poales_odb10
Completenessi <p>Complete Proteome Detector (CPD) is an algorithm which employs statistical evaluation of the completeness and quality of proteomes in UniProt, by looking at the sizes of taxonomically close proteomes. Possible values are 'Standard', 'Close to Standard' and 'Outlier'.</p> Outlier (high value)

Oryza sativa (rice) is a monocotyledonous flowering plant of the family Poaceae and is one of the most important crop plants in the world, providing the principal food source for half of the world's population.

Oryza sativa subsp. japonica is one of three major subspecies of rice, the others being indica and javanica. Oryza sativa subsp. japonica is short-grained and high in amylopectin so that the grains stick together when cooked, which distinguishes it from subsp. indica which is long grained and not sticky.

Oryza sativa subsp. japonica is grown in dry fields, mainly in temperate or colder climates such as Japan.

Oryza sativa has a haploid chromosome number of 12, containing 370 Mb with 30,000 protein-coding genes. Rice was an obvious choice for the first whole genome sequencing of a cereal crop. It is the smallest of the major cereal crop genomes and is the easiest to transform genetically. The cultivar sequenced from the japonica subspecies was Nipponbare (www.thericejournal.com/content/6/1/4/abstract).

Componentsi <p>Genomic components encoding the proteome</p>

Component nameGenome Accession(s)
Component representationProteins
Chromosome 1
AP008207
5808
Chromosome 2
AP008208
7050
Chromosome 3
AP008209
6925
Chromosome 4
AP008210
5852
Chromosome 5
AP008211
4173
Chromosome 6
AP008212
5906
Chromosome 7
AP008213
5556
Chromosome 8
AP008214
4956
Chromosome 9
AP008215
3948
Chromosome 10
AP008216
4298
Chromosome 11
AP008217
3376
Chromosome 12
AP008218
1631

Publications

  2. "The rice annotation project database (RAP-DB): 2008 update."
    The rice annotation project (RAP)
    Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [Abstract]
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