Cave fish assembly and gene annotation


The blind cave fish (Astyanax mexicanus) genome sequence was produced by Washington University. The genome is 1Gb in length, consisting of 10,735 toplevel sequences, all of which are unplaced scaffolds (from 121,345 contigs). The N50 of the scaffolds is 1.5 Mb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000372685.1

Gene annotation

The gene set was built using a mixed approach. Due to the lack of species specific sequences and the availability of RNASeq data for blind cave fish from Washington University, the final gene set comprises models based on orthologous proteins from the vertebrate division of UniProtKB, longest translations of some stickleback and zebrafish gene models from Ensembl 72, as well as models from RNASeq data.

The RNASeq data only contained samples from the entire organism, not individual tissues. 13,097 gene models were made exclusively from RNASeq data. The data were also used to add UTR to gene models. The total gene set contains 23,042 protein-coding genes with a further 709 ncRNAs and 21 pseudogenes. You can find more information on how we build the gene models from RNASeq data here.

More information

General information about this species can be found in Wikipedia.



AssemblyAstMex102, INSDC Assembly GCA_000372685.1, Apr 2013
Database version80.102
Base Pairs964,248,202
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).

Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedApr 2013
Genebuild releasedDec 2013
Genebuild last updated/patchedDec 2013

Gene counts

Coding genes

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

Non coding genes709
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.

Misc non coding genes15

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.

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.24,428


Genscan gene predictions39,152