Cat assembly and gene annotation

Assembly

The Felis_catus-6.2 assembly of the cat (Felis catus) genome was produced by the International Cat Genome Sequencing Consortium. The whole assembly is composed of 19 chromosomes and plasmids, 6399 scaffolds with a N50 value of 4.7Mb and 203082 contigs with a N50 value of 20.6kb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000181335.2

Gene annotation

Felis_catus-6.2 was annotated using a standard Ensembl mammalian genebuild pipeline, incorporating RNA-seq data provided by The Texas A&M College of Veterinary Medicine & Biomedical Sciences, Department of Veterinary Integrative Biosciences. The final gene set is made up from 19493 protein coding genes, 542 pseudogenes, and 1855 non-coding RNA genes.

RNASeq data set

As part of the main gene set, we have predicted gene models based on RNA-seq data from testis tissue of four individuals (unpaired 50bp reads) using the RNA-Seq pipeline. We did similarity matching (BLASTp) of these models against UniProt proteins having evidence of existence on protein or transcript level (protein existence level 1 and 2) in order to confirm the open reading frame (ORF). A total of 3504 RNA-seq transcript models were used in the final gene set. The data was also used to add UTR to gene models.

In addition to the main gene set, the Ensembl RNA-seq pipeline built the following numbers of gene models for each of the four individuals and for the merged data set:

IndividualNumber of gene models
FCA_237223963
FCA_237324114
FCA_299624080
FCA_404824816
Merged dataset25709

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyFelis_catus_6.2, INSDC Assembly GCA_000181335.2, Sep 2011
Database version78.62
Base Pairs2,365,745,914
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).

2,455,541,136
Genebuild byEnsembl
Genebuild methodMixed strategy build
Genebuild startedDec 2011
Genebuild releasedJan 2013
Genebuild last updated/patchedJan 2013

Gene counts

Coding genes

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

19,493
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.

1,855
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.

542
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.22,656

Other

Genscan gene predictions45,433
Short Variants324,963