RPP25 Gene

Name	ribonuclease P/MRP 25kDa subunit
Description	Enables ribonuclease P RNA binding activity. Contributes to ribonuclease P activity. Involved in tRNA 5'-leader removal. Located in centriolar satellite and nucleoplasm. Part of multimeric ribonuclease P complex and ribonuclease MRP complex. Biomarker of autistic disorder. [provided by Alliance of Genome Resources, Mar 2025]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nRPP25 is an essential 25‐kDa protein subunit of the human RNase P and RNase MRP endoribonucleoprotein complexes that mediate the processing of tRNA, precursor ribosomal RNA, and other RNA substrates. It forms a heterodimer with RPP20, with their association—mediated primarily by conserved Alba‐type core domains—being critical for high-affinity binding to the P3 region of the RNA subunit. Detailed structural and biochemical analyses have revealed that this heterodimer not only governs RNA recognition and enzyme assembly but also appears to have evolved from archaeal Alba proteins, adapting its quaternary interactions to support functions unique to eukaryotic ribonucleoprotein complexes, including potentially mediating the dimerization of the RNase MRP complex."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its canonical role in RNA processing, dysregulation of RPP25 has been implicated in diverse pathological contexts. In autoimmunity, autoantibodies directed against RPP25 are under evaluation as potential biomarkers for systemic sclerosis, as it is a key component of the Th/To complex. In neurodevelopment, reduced transcript levels of RPP25 in the prefrontal cortex of subjects with autism suggest a nuanced role during late fetal brain development, even though the protein remains undetectable. Moreover, in cervical cancer, deregulation of RPP25 through a long non-coding RNA/miRNA-mediated axis has been shown to impact cell migration, invasion, and epithelial-to-mesenchymal transition, thereby contributing to tumor progression."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "4", "end_ref": "6"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Katherine L D Hands-Taylor, Luigi Martino, Renée Tata, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Heterodimerization of the human RNase P/MRP subunits Rpp20 and Rpp25 is a prerequisite for interaction with the P3 arm of RNase MRP RNA."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleic Acids Res (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/nar/gkq141"}], "href": "https://doi.org/10.1093/nar/gkq141"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20215441"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20215441"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Clarence W Chan, Benjamin R Kiesel, Alfonso Mondragón "}, {"type": "b", "children": [{"type": "t", "text": "Crystal Structure of Human Rpp20/Rpp25 Reveals Quaternary Level Adaptation of the Alba Scaffold as Structural Basis for Single-stranded RNA Binding."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Mol Biol (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jmb.2018.03.029"}], "href": "https://doi.org/10.1016/j.jmb.2018.03.029"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29625199"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29625199"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Changping Yin, Guohui Bai, Yuzhu Zhang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Crystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncRNA RMRP."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Struct Biol (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jsb.2021.107704"}], "href": "https://doi.org/10.1016/j.jsb.2021.107704"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33571640"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33571640"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Hsien-Sung Huang, Iris Cheung, Schahram Akbarian "}, {"type": "b", "children": [{"type": "t", "text": "RPP25 is developmentally regulated in prefrontal cortex and expressed at decreased levels in autism spectrum disorder."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Autism Res (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/aur.141"}], "href": "https://doi.org/10.1002/aur.141"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20632321"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20632321"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Michael Mahler, Cristina Gascon, Sima Patel, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Rpp25 is a major target of autoantibodies to the Th/To complex as measured by a novel chemiluminescent assay."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Arthritis Res Ther (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/ar4210"}], "href": "https://doi.org/10.1186/ar4210"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23587095"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23587095"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Jian Yang, Shunyu Hou, Baoquan Liang "}, {"type": "b", "children": [{"type": "t", "text": "LINC00319 promotes migration, invasion and epithelial-mesenchymal transition process in cervical cancer by regulating miR-3127-5p/RPP25 axis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "In Vitro Cell Dev Biol Anim (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s11626-019-00425-5"}], "href": "https://doi.org/10.1007/s11626-019-00425-5"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31942724"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31942724"}]}]}]}
Proteins	RPP25_HUMAN
NCBI Gene ID	54913
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

RPP25 has 4,877 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 109 datasets.

Click the + buttons to view associations for RPP25 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

RPP25 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by RPP25 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of RPP25 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of RPP25 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of RPP25 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of RPP25 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of RPP25 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of RPP25 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of RPP25 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of RPP25 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of RPP25 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of RPP25 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of RPP25 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of RPP25 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with RPP25 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with RPP25 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of RPP25 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of RPP25 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of RPP25 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of RPP25 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing RPP25 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing RPP25 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing RPP25 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with RPP25 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with RPP25 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	CORUM Protein Complexes	protein complexs containing RPP25 protein from the CORUM Protein Complexes dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of RPP25 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with RPP25 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with RPP25 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with RPP25 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of RPP25 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by RPP25 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with RPP25 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with RPP25 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with RPP25 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with RPP25 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with RPP25 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at RPP25 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of RPP25 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of RPP25 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing RPP25 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.