New Ensembl Pre! sites

The Ensembl Pre! site has been updated for four species: zebrafish (Danio rerio), rat (Rattus norvegicus), sperm whale (Physeter macrocephalus) and fugu (Takifugu rubripes).

Sperm whale is a new species to Ensembl. Our main site already displays earlier assemblies for fugu, zebrafish and rat.

Zebrafish

ZebrafischThe zebrafish assembly, GRCz10 (GCA_000002035.3), was made available by The Genome Reference Consortium in September 2014. Since the previous release, Zv9 in July 2010, the GRC has taken over the task of improving and maintaining the zebrafish assembly. The most notable changes in the chromosome landscape since the previous release can be found on chromosome 4, which has gained about 15 Mb in length. Furthermore, 94 of the 112 previously unplaced contigs are now located on chromosomes. In total, this assembly consists of 26 chromosomes and 3,399 unplaced scaffolds. The full annotation of an older zebrafish assembly, Zv9, can be found on our main website. Click here to go to the zebrafish Pre! site, where you can view alignments of zebrafish UniProt proteins and human Ensembl translations, as well as gene models projected from the previous zebrafish assembly.

Rat

rattusThe new rat assembly, Rnor_6.0 (GCA_000001895.4), was produced by The Rat Genome Sequencing and Mapping Consortium and was released in July 2014. This assembly comprises 954 toplevel sequences, 22 of which are chromosomes (chromosome Y is a new addition in this assembly), and 1,395 of which are unplaced scaffolds. The full annotation of an older rat assembly, Rnor_5.0, can be found on our main website. Otherwise, click here to visit the rat Pre! site, where you can view alignments of rat UniProt proteins and human and mouse Ensembl translations, as well as gene models projected from the previous rat assembly.

Sperm Whale

800px-Mother_and_baby_sperm_whaleThe sperm whale assembly, PhyMac_2.0.2 (GCA_000472045.1), was produced in September 2013 by The Aquatic Genome Models Consortium. The assembly does not contain any assembled chromosomes or linkage groups and is instead made up of 11,711 unplaced scaffolds. The species is an important model for a number of human conditions such as respiratory disease, metal toxicity and cancer. For example, sperm whales exposed to high levels of chromium have no adverse health effects whereas humans do. Studying this species could lead to development of treatments for human chromium-related disorders. Click here to visit the sperm whale Pre! site, where you can view alignments of human and dolphin Ensembl translations.

Fugu

fugu_tThe fugu genome assembly, FUGU5 (GCA_000180615.2), was released in October 2011 by The Fugu Genome Sequencing Consortium. It is composed of 22 autosomal chromosomes, with a total sequence length of 391Mb. The species was initially proposed as a useful model for annotating and understanding the human genome, as it contains a similar repertoire of genes to human yet is only roughly one-eighth of the size. It is among the smallest vertebrate genomes, and previous assemblies of this species have already shown themselves to be useful reference genomes for identifying genes and other functional elements in other vertebrate species. The full annotation of an older fugu assembly, FUGU 4.0, can be found on our main website. Click here to visit the fugu Pre! site, where you can view alignments of human and dolphin Ensembl translations.

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