# Providing Standardized Gene Nomenclature for Domestic Ungulate Scavenger Receptor Genes

**Authors:** Jessica Cruz, Fiona McCarthy

PMC · DOI: 10.17912/micropub.biology.001584 · microPublication Biology · 2025-06-24

## TL;DR

This paper establishes standardized naming for scavenger receptor genes in domestic ungulates, including newly identified ones and previously studied WC1 genes.

## Contribution

The study introduces standardized nomenclature for novel and previously unstudied scavenger receptor genes in ungulates.

## Key findings

- Twenty-seven SCAR genes common to all five studied ungulate species were identified and classified.
- Standardized nomenclature was provided for Workshop Cluster 1 (WC1) genes absent in model organisms.
- The study focuses on agriculturally important ungulate species for gene classification.

## Abstract

Scavenger Receptor (SCAR) genes are a heterogeneous group involved in innate immunity and immunomodulation. While standardized gene nomenclature is provided for model organism SCAR genes, ungulates have novel SCAR genes which have not been systematically classified. This study compares SCAR genes for five representative ungulate species which are selected based on their agricultural importance and representation. We identify and classify twenty-seven SCAR genes common to all species and provide standardized gene nomenclature for genes novel to these ungulate species. Notably, we provide standardized gene nomenclature for the previously studied Workshop Cluster 1 (WC1) genes which are absent in model organisms.

## Linked entities

- **Genes:** RPS4X (ribosomal protein S4 X-linked) [NCBI Gene 6191], ATP7B (ATPase copper transporting beta) [NCBI Gene 540]

## Full-text entities

- **Genes:** CD163L1 (CD163 molecule-like 1) [NCBI Gene 100144477] {aka WC1}, CLEC4D (C-type lectin domain family 4 member D) [NCBI Gene 338339] {aka CD368, CLEC-6, CLEC6, CLECSF8, Dectin-3, MCL}, CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, CLSTN3 (calsyntenin 3) [NCBI Gene 9746] {aka CDHR14, CSTN3, alcbeta}, PEX5 (peroxisomal biogenesis factor 5) [NCBI Gene 5830] {aka PBD2A, PBD2B, PTS1-BP, PTS1R, PXR1, RCDP5}, RPS4X (ribosomal protein S4 X-linked) [NCBI Gene 6191] {aka CCG2, DXS306, RPS4, S4, SCAR, SCR10}, RBP5 (retinol binding protein 5) [NCBI Gene 100270724], CLSTN3 (calsyntenin 3) [NCBI Gene 100511695], CD163L1 (CD163 molecule like 1) [NCBI Gene 283316] {aka CD163B, M160, SCARI2, WC1}, RBP5 (retinol binding protein 5) [NCBI Gene 83758] {aka CRBP-III, CRBP3, CRBPIII, HRBPiso}, CLEC6A (C-type lectin domain containing 6A) [NCBI Gene 93978] {aka CLEC4N, CLECSF10, dectin-2, hDECTIN-2}, CLEC4E (C-type lectin domain family 4 member E) [NCBI Gene 26253] {aka CLECSF9, MINCLE}, HLA-C (major histocompatibility complex, class I, C) [NCBI Gene 3107] {aka D6S204, HLA-JY3, HLAC, HLC-C, MHC, PSORS1}, CD4 (CD4 molecule) [NCBI Gene 920] {aka CD4mut, IMD79, Leu-3, OKT4D, T4}, CD163 (CD163 molecule) [NCBI Gene 397031], SCART1 (scavenger receptor family member expressed on T cells 1) [NCBI Gene 619207], ATP7B (ATPase copper transporting beta) [NCBI Gene 540] {aka PWD, WC1, WD, WND}, APP (amyloid beta precursor protein) [NCBI Gene 351] {aka AAA, ABETA, ABPP, AD1, APPI, CTFgamma}, PEX5 (peroxisomal biogenesis factor 5) [NCBI Gene 100512963]
- **Diseases:** inflammatory (MESH:D007249)
- **Species:** Ovis aries (domestic sheep, species) [taxon 9940], Bos taurus (bovine, species) [taxon 9913], Capra hircus (domestic goat, species) [taxon 9925], Homo sapiens (human, species) [taxon 9606], Sus scrofa (pig, species) [taxon 9823], Equus caballus (domestic horse, species) [taxon 9796]

## Full text

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## Figures

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## References

19 references — full list in the complete paper: https://tomesphere.com/paper/PMC12235456/full.md

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Source: https://tomesphere.com/paper/PMC12235456