Protein coding sequences (CDS) of the genome of a Peromyscus leucopus
Data files
May 01, 2026 version files 867.73 KB
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CDS_Pleuc_names_v7.xlsx
866.26 KB
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README.md
1.47 KB
Abstract
This table provides curated gene annotations for 22,654 protein-coding sequences (CDS) in the Peromyscus leucopus genome. Many original CDS were assigned placeholder names (e.g., “LOC1146xxxxx”) by the NCBI vertebrate genome annotation pipeline. To facilitate downstream analyses, including differential gene expression analysis, these were manually annotated with gene symbols based on sequence similarity to Mus musculus proteins. BLASTx was used to search each CDS against the non-redundant Mus musculus protein database in GenBank. Gene names were assigned based on the highest-confidence matches, using default BLASTx parameters. Annotation was performed iteratively as genes of interest were identified in expression analyses.
Title:
Manually curated gene names for Peromyscus leucopus protein-coding sequences
Organism:
Peromyscus leucopus (LL stock female)
Reference Genome:
GenBank accession: GCF_004664715.2
Source: Long et al., 2019
File:
CDS_Pleuc_names_v7.xlsx
This Excel file provides curated gene annotations for 22,654 protein-coding sequences (CDS) from the P. leucopus genome.
Many CDS originally lacked gene names and were assigned placeholder “LOC” designations by the NCBI annotation pipeline.
Using BLASTx against the non-redundant Mus musculus protein database, ~1,000 “LOC” entries were assigned gene names.
This annotation was used to support RNA-seq analysis in lung and brain tissues.
Contents:
CDS_Pleuc_names_v7.xlsx
Variables (Columns):
- gene: Curated gene name assigned via BLASTx match to Mus musculus protein (string)
- reference: GenBank accession and contig information for the CDS and protein product (string)
- loc_add: Original NCBI LOC designation for the CDS (string)
- Size: Length of coding sequence (CDS) in base pairs (integer)
Units:
- Size is measured in base pairs (bp)
Missing Data:
- Missing entries in columns such as
loc_addare indicated by blank cells.
Recommended Citation:
If using this dataset, please cite:
Long, A. et al. (2019). Genomic resources for Peromyscus leucopus, the white-footed deermouse. GenBank accession GCF_004664715.2.