The new chromosome-scale assembly AmexG_v6 reported by Schloissnig et al 2021 and various data tracks can be accessed through the following genome hub link to the UCSC Genome Browser. Please see fair use statements below.

The previous  Amex_PQ.v4 chromosomal scale assembly reported by Smith et al 2019 can be accessed through the following genome hub link to the UCSC Genome Browser. 

Variant and SNP density track session from Timoshevskaya et al 2020 (read-only access to full text). New analogous tracks are also available on the V6 browser.

EMBARGO/FAIR USE OF EPIGENETICS DATA: We are delighted to release unpublished epigenetics tracks to the community. We encourage others to use these data, but in doing so we also expect that they will respect our right to first presentation (including journal publications, pre-prints such as in bioRxiv, public conference talks, and press releases) of a genome-wide analysis of these tracks. This includes the use of genome-wide epigenetics data for generalized descriptions of gene-regulatory patterns in axolotl and evolutionary/developmental/regeneration analyses, on behalf of ourselves as data producers and collaborators. Therefore, please respect the embargo on the presentation of analyses using pre-publication data that we release via this website and relevant archives. Similar fair use statements apply to many genome assemblies such as those released by the Sanger Institute and the VGP.

Exceptions to the policy are for analyses of either a single locus, or a single gene family, or for use as a reference for mapping reads from independent studies. Individual tracks and datasets will be considered released from this embargo when they are expressly published, and the relevant reference(s) will be added to this website at that time. For any queries about using the data, referencing/publishing analyses based on pre-publication data or interest in contributing to genome-scale analyses please contact  This email address is being protected from spambots. You need JavaScript enabled to view it..  We are also happy to make tracks from other groups available under this same fair use policy.

We provide three assemblies for BLAST search of the A. mexicanum genome. To get search results faster, limit the number of sequences in your query and number of reported alignments (set smaller value for the -num_alignments parameter). When searching oligonucleotides (PCR primers, gRNAs) for off-target alignments, use the following command: word_size 11.

1. The AmexG_v6 database was built from a chromosomal scale assembly reported by Schloissnig et al 2021. This assembly was generated from DNA sequences obtained from a single white (d/d) male axolotl. The assembly also includes the mitochondrial genome.

2. The Amex_PQ.v4 database was built from a chromosomal scale assembly reported by Smith et al 2019.

Gene and EST Database

Assembly V4.0: The A. mexicanum transcriptome has been deep sequenced (15,000,000 Roche 454 short sequence reads and 50K Sanger reads) and assembled. The resulting assembly V4.0 can now be BLAST searched here. Approximately 89.9% of the 14 million high quality sequences were assembled into contigs with a total length of 542 Mb.

Gene Expression

The analysis of gene expression is being studied using microarray, quantitative-realtime PCR, RNA-Seq, and Nanostring. These resources include: