DOI: 10.5281/zenodo.17752473
title: Domain-Level Annotation and Conservation of Mouse Endogenous Retroviruses in the GRCm39 Genome

description: 💡 Introduction

This dataset provides a comprehensive, genome-wide annotation of conserved retroviral protein domains within mouse endogenous retroviruses (MERVs) mapped to the GRCm39 reference genome. Using the same fully reproducible pipeline applied to the human (GRCh38 and T2T-CHM13) datasets—based on RepeatMasker, EMBOSS getorf, HMMER, and InterProScan—we identified and annotated all open reading frames (ORFs) predicted within internal ERV regions across the mouse genome.

Mouse ERVs are more numerous and structurally diverse than their human counterparts, reflecting lineage-specific expansion of families such as ERVL, ERVL-MaLR, IAPE, MERVL, RLTR, ORR1, and MMERVK10C. This dataset captures this diversity, recovering 47,840 retroviral-like domain hits, including conserved domains from reverse transcriptase, RNase H, integrase, protease, Gag, Env, and several accessory gene families characteristic of murine ERVs. As in the human analysis, many domains show moderate to high HMMER coverage, enabling identification of ORFs with extensive structural preservation.

InterProScan and Phobius predictions were integrated to recover catalytic residues, zinc-binding motifs, heptad repeats, signal peptides, and transmembrane helices—providing a multi-layered annotation of the coding potential of individual ERV loci, including those specific to the mouse lineage.

🔭 Integration into HERVarium

This dataset forms the mouse internal-domain component of HERVarium, complementing the human (GRCh38 and T2T) datasets and extending the resource to a second mammalian species. HERVarium integrates:



internal region protein-domain annotations (this dataset), and

LTR structural and regulatory annotations (will be released separately).


Together, these datasets will provide a unified comparative framework for studying ERV evolution, coding potential, and regulatory co-option across mammals.

🧬 The dataset includes:



BED files with genomic coordinates of annotated ERV domains

FASTA files containing predicted ORFs and extracted domain sequences

InterProScan results for structural and functional annotation

Phobius predictions for Env-related transmembrane/coiled-coil domains

Summary tables describing domain conservation, co-occurrence patterns, and lineage-specific features

RepeatMasker output for GRCm39 used in the analysis

The GyDB HMM database and classification file, required to reproduce the pipeline


These resources provide the most detailed map to date of protein-domain conservation in mouse ERVs and serve as a foundation for comparative ERV genomics between mouse and human.

📄 Description of each file



ERV_mouse_internal_sequences.fasta: nucleotide sequences of merged internal ERV regions extracted from GRCm39 RepeatMasker annotations.

ERV_mouse_orfs_aa_sequences.fasta: amino acid sequences of predicted ORFs within internal regions.

ERV_mouse_hmmscan_output.tbl: raw hmmscan results with all GyDB profile matches.

ERV_mouse_annotated_domains.tsv: filtered table summarizing the best conserved domain per domain class per ORF.

ERV_mouse_domains.bed: genome coordinates of all mapped domains.

ERV_mouse_domains_nt_sequences.fasta: nucleotide sequences of ERV domain regions.

ERV_mouse_domains_aa_sequences.fasta: amino acid sequences corresponding to domain regions.

ERV_mouse_interproscan_output.zip: full InterProScan directory with XML/TSV outputs.

ERV_mouse_interproscan_cdd_parsed.tsv: summary of conserved domain database (CDD) annotations.

ENV_phobius_mouse_output.txt: Phobius predictions for Env-containing ORFs.

ERV_mouse_internal.bed: BED file with genomic coordinates of internal ERV regions reconstructed from RepeatMasker annotations.

gydb_domains_classification.tsv: mapping of GyDB HMM profile names to GAG/POL/ENV/Accessory/Other.

combined_gydb.hmm: concatenated HMM database used for domain detection.

GRCm39.primary_assembly.genome.fa.out.tar.xz: RepeatMasker output used to define internal regions.


💻 Code and citation

This dataset was generated using the same reproducible pipeline developed for the human analyses, available at:🔗 https://github.com/funcgen/herv-domain-map

If you use this dataset, please cite both the dataset DOI and the corresponding human article:



Montserrat-Ayuso, T., & Esteve-Codina, A. (2025). A comprehensive annotation of conserved protein domains in human endogenous retroviruses. bioRxiv. https://doi.org/10.1101/2025.07.25.666750


While mouse-specific manuscript text may be added later, this article describes the overall pipeline.

 

Version history

v1: Initial release of internal-region annotations and domain-level conservation mapped to the GRCm39 genome. Includes all domain annotation pipeline outputs, InterProScan and Phobius predictions, and the RepeatMasker output used in the analysis.