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StatusReference proteome
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> 21,751
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="">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>UP000008549
Taxonomy6238 - Caenorhabditis briggsae
Last modifiedJanuary 29, 2021
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="">more...</a>)</p> GCA_000004555.3 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 (F) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment.</p> C:98.1%[S:97.1%,D:0.9%],F:0.9%,M:1%,n:3131 nematoda_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> Standard

Caenorhabditis briggsae is a nematode roundworm that is almost indistinguishable from the model-organism nematode Caenorhabditis elegans. It also shares many other features such as chromosome number, habitat and behavior which make it an ideal candidate for comparative genomics studies, especially as 93% of the predicted protein-coding genes have clear C. elegans orthologs.

Like C. elegans the C. briggsae embryo goes through four larval stages before becoming a mature adult. In response to over-crowding or an inadequate food supply the worm can adopt a dauer larval stage. In this stage the worm can survive for up to three months. Most worms are found in this stage. Sexual reproduction occurs by an adult hermaphrodite self-fertilizing.

The reference proteome for C. briggsae (strain AF16) is derived from a hybrid sequencing approach combining whole-genome assembly with whole-genome shotgun sequencing (WGS). The C. briggsae genome size is approximately 104 Mb, slightly larger than that of the C. elegans. The difference is mainly due to the larger non-genic repetitive DNA content in C. briggsae's genome. The number of protein-coding genes is estimated to be 19,507.

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome I3074
Chromosome II3325
Chromosome III2887
Chromosome IV3265
Chromosome V4771
Chromosome X3749
Unassembled WGS sequence1252
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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