Phylogenetic Analyses of Vertebrate L-Type Calcium Channel Alpha 1 Subunits

Phylogenetic analyses of vertebrate voltage-gated calcium channel alpha 1 subunits (CACNA1S, CACNA1C, CACNA1D, CACNA1F) using amino acid sequences predicted from the Ensembl genome browser. The dataset includes species and genome assembly information, database identifiers, location data, annotation notes, sequence alignments, and phylogenetic trees. It was created by Jenny Widmark and is available via paperswithcode under an Open Access license.

Use Cases

• Constructing phylogenetic trees based on the provided multiple sequence alignment of CACNA1 subunits.
• Studying gene family evolution across vertebrate species listed in the description, including human, mouse, chicken, and zebrafish.
• Curating and verifying gene predictions for calcium channel sequences using the described manual and automated methods.
• Benchmarking phylogenetic inference algorithms using the included neighbor-joining and maximum likelihood tree files.

Strengths

• Includes data for 11 distinct species, from human to fruit fly, providing a broad evolutionary perspective.
• Provides multiple data artifacts: a curated sequence alignment, phylogenetic trees in standard formats (Newick/Phylip), and supplementary tables with identifiers and annotations.
• Documents specific bioinformatics tools and parameters used for alignment (ClustalX) and tree construction (PhyML, neighbor-joining with 1000 bootstrap replicates).

Limitations

• Row count and dataset size are unknown, which may limit suitability assessment for large-scale analyses.
• Column-level documentation is absent; field semantics must be inferred from the supplementary Excel file after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

Ensembl genome browser

Collection Method

Sequences were extracted from Ensembl, with additional curation using Genscan and manual inspection. Phylogenetic analyses were performed using ClustalX and PhyML.