Axolotls can be used to efficiently screen chemicals for toxicity and effects on tissue regeneration. This database reports chemicals that were screened using an axolotl embryo tail regeneration model. Chemical outcomes on tail regeneration were classified as either inhibitory, non-inhibitory, or toxic, and chemicals that were validated in a second screen are noted. The database can be searched using a chemical's name, structure (SMILES), molecular weight (ML), or bioactivity.
For more details about the chemical screening project, click here.
To learn how to perform the axolotl embryo tail regeneration assay, click here.
Search for Chemical Name/SMILES/MW/Bioactivity
Chemical Name = Romidepsin
SMILES = C\C=C1\NC(=O)[C@H]2CSSCC\C=C\[C@H](CC(=O)N[C@@H](C(C)C)C(=O)N2)OC(=O)[C@@H](NC1=O)C(C)C
MW = 540.69
Bioactivity = Histone deacetylase inhibitor (HDAC)
Outcome = Inhibits tail regeneration at 10 uM
Validated = Yes
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.
1. The Amex_PQ.v4 database was built from a chromosomal scale assembly reported by Smith et al 2019. For small chromosomes, the results of BLAST searches are reported for the entire chromosome. For large chromosomes, the results of BLAST searches are reported for P or Q chromosome arms, or regions within P or Q chromosome arms.
For example, Chr1P is split into Chr1P:0-1,000,000,000 and Chr1P:1,000,000,000-1,477,091,900. In this case, alignments are reported relative to the position 0 or 1,000,000,000. A Chr1P alignment spanning 4,500 - 5,300 will be reported as either Chr1P:4500-5300 or Chr1P:1,000,004,500-1,000,005,300.
3. The Amex_female.v1 database was built from an assembly used by Keinath et al 2018 to identify the sex-determining region in the axolotl genome.
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.
We provide NCBI- BLAST (Basic Local Alignment Search Tool) to compare nucleotide or protein sequences to our EST sequence databases. BLAST can be used to infer functional and evolutionary relationships between sequences and help identify members of gene families.