Caenorhabditis elegans assembly and gene annotation

Assembly

Genome sequence and annotation have been imported from the WS245 release of WormBase (which includes the WBcel235 version of the C.elegans reference genome). Included are annotated operons, genes, transcripts and translations, as well as RNAi and BLAST/BLAT homology data. In addition Affymetrix and Agilent cross references for C.elegans expression arrays have been added.

We include C.elegans in Ensembl (and also Ensembl Genomes) to allow people to access the data through the Ensembl user interface (both for visualisation and data mining) and to provide cross-species integration through our comparative genomics resources (such as homologous gene links and protein family pages).

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000002985.3

Gene annotation

This species and other invertebrates are also available from our sister site, Ensembl Metazoa

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyWBcel235, INSDC Assembly GCA_000002985.3, Dec 2012
Database version78.245
Base Pairs103,022,290
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

100,286,401
Genebuild byWormBase
Genebuild methodImport
Genebuild startedSep 2014
Genebuild releasedOct 2014
Genebuild last updated/patchedOct 2014

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

20,447
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

24,443
Long non coding genes

Long non coding genes are usually greater than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as long non coding genes: 3prime_overlapping_ncrna, ambiguous_orf, antisense, antisense_RNA, lincRNA, ncrna_host, non_coding, non_stop_decay, processed_transcript, retained_intron, sense_intronic, sense_overlapping. The majority of the long non coding genes in Ensembl are annotated manually by HAVANA.

268
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

1,590
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.57,834