Culex quinquefasciatus (CpipJ2)

Culex quinquefasciatus Assembly and Gene Annotation

The Culex quinquefasciatus data and its display on Ensembl Genomes are made possible through a joint effort by the Ensembl Genomes group and VectorBase, a component of VEuPathDB.

About Culex quinquefasciatus

Culex quinquefasciatus, the Southern House Mosquito, is the vector responsible for transmission of filariasis and a number of viruses including West Nile virus, St. Louis encephalitis and Japanese encephalitis.

Picture credit (public domain): James Gathany (CDC) 2001


The Culex quinquefasciatus Johannesburg strain genome sequence is a joint effort between the Broad Institute and the J. Craig Venter Institute (JCVI). Assembly of 8x shotgun coverage was performed using the Broad's whole genome assembly package ARACHNE. The assembly presented here (CpipJ2, April 2014) consists of 3,171 supercontigs and a mitochondrial chromosome, totalling 580 Mb.


The annotation of the C. quinquefasciatus genome is a collaboration between VectorBase, JCVI and the Broad Institute. Each group generated a set of gene predictions which were merged into a single canonical set [1]. The gene set currently shown (CpipJ2.5, July 2019) is an improved version of the initial set, with integration of community manual annotations and non-coding RNA genes from the Ensembl Genomes pipeline.


  1. Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.
    Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Camara F et al. 2010. Science. 330:86-88.



AssemblyCpipJ2, INSDC Assembly GCA_000209185.1, Jan 2007
Database version106.3
Golden Path Length579,057,705
Genebuild byVEuPathDB
Genebuild methodFull genebuild
Data sourceVectorBase

Gene counts

Coding genes18,965
Non coding genes828
Small non coding genes826
Long non coding genes2
Gene transcripts19,866


Short Variants5,940

About this species