RBMXL3 Gene

HGNC Family	RNA binding motif containing (RBM)
Name	RNA binding motif protein, X-linked-like 3
Description	Predicted to enable mRNA binding activity and snRNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. [provided by Alliance of Genome Resources, Mar 2025]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nRecent studies highlight diverse mechanisms of gene regulation underlying cellular differentiation and function. For example, chromatin remodeling complexes, such as the SWI/SNF/BAF complex modulated by BCL7A, play a key role in neural progenitor cell commitment and neuronal plasticity by coordinating mitochondrial bioenergetics and precise transcriptional programs. This work underscores the importance of integrating metabolic cues with cell-intrinsic transcriptional processes to control cell fate decisions in the nervous system."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn parallel, a distinct regulatory mechanism has been uncovered in pulmonary biology where post‐transcriptional control is critical. Here, a primate‐specific RNA-binding protein, RBMXL3, has been shown to bind a 30-nucleotide hairpin element (RBE) located in the 3′-untranslated region of human surfactant protein B (SP‐B) mRNA. Under basal conditions, the RBE recruits decay factors that reduce intrinsic mRNA stability; however, upon dexamethasone treatment, enhanced binding of RBMXL3 relieves this decay, thereby stabilizing SP‐B mRNA and promoting its expression in lung epithelial cells. These findings reveal a novel mechanism by which RBMXL3 modulates mRNA stability in response to hormonal signals, contributing to the proper function of pulmonary surfactant systems."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Lena Wischhof, Hang-Mao Lee, Janine Tutas, et al. "}, {"type": "b", "children": [{"type": "t", "text": "BCL7A-containing SWI/SNF/BAF complexes modulate mitochondrial bioenergetics during neural progenitor differentiation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "EMBO J (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.15252/embj.2022110595"}], "href": "https://doi.org/10.15252/embj.2022110595"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "36305367"}], "href": "https://pubmed.ncbi.nlm.nih.gov/36305367"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Lidan Liu, Xiangli Liu, Weizhen Bi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A primate-specific RNA-binding protein (RBMXL3) is involved in glucocorticoid regulation of human pulmonary surfactant protein B (SP-B) mRNA stability."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Physiol Lung Cell Mol Physiol (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1152/ajplung.00022.2020"}], "href": "https://doi.org/10.1152/ajplung.00022.2020"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33719563"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33719563"}]}]}]}
Synonyms	CXORF55
Proteins	RMXL3_HUMAN
NCBI Gene ID	139804
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

RBMXL3 has 1,159 functional associations with biological entities spanning 8 categories (molecular profile, organism, functional term, phrase or reference, chemical, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 52 datasets.

Click the + buttons to view associations for RBMXL3 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

RBMXL3 Gene

Functional Associations

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

	Dataset	Summary
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of RBMXL3 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 RBMXL3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of RBMXL3 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of RBMXL3 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of RBMXL3 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with RBMXL3 protein from the CCLE Cell Line Proteomics dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of RBMXL3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	gene perturbations changing expression of RBMXL3 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with RBMXL3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of RBMXL3 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with RBMXL3 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of RBMXL3 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 RBMXL3 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with RBMXL3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at RBMXL3 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 RBMXL3 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of RBMXL3 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	GEO Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of RBMXL3 gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset.
	GEO Signatures of Differentially Expressed Genes for Viral Infections	virus perturbations changing expression of RBMXL3 gene from the GEO Signatures of Differentially Expressed Genes for Viral Infections dataset.
	GO Biological Process Annotations 2023	biological processes involving RBMXL3 gene from the curated GO Biological Process Annotations 2023 dataset.
	GO Biological Process Annotations 2025	biological processes involving RBMXL3 gene from the curated GO Biological Process Annotations2025 dataset.
	GO Cellular Component Annotations 2023	cellular components containing RBMXL3 protein from the curated GO Cellular Component Annotations 2023 dataset.
	GO Molecular Function Annotations 2015	molecular functions performed by RBMXL3 gene from the curated GO Molecular Function Annotations 2015 dataset.
	GO Molecular Function Annotations 2023	molecular functions performed by RBMXL3 gene from the curated GO Molecular Function Annotations 2023 dataset.
	GO Molecular Function Annotations 2025	molecular functions performed by RBMXL3 gene from the curated GO Molecular Function Annotations 2025 dataset.
	GTEx Tissue Gene Expression Profiles	tissues with high or low expression of RBMXL3 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles dataset.
	GTEx Tissue Gene Expression Profiles 2023	tissues with high or low expression of RBMXL3 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
	HPA Tissue Protein Expression Profiles	tissues with high or low expression of RBMXL3 protein relative to other tissues from the HPA Tissue Protein Expression Profiles dataset.
	InterPro Predicted Protein Domain Annotations	protein domains predicted for RBMXL3 protein from the InterPro Predicted Protein Domain Annotations dataset.
	JASPAR Predicted Human Transcription Factor Targets 2025	transcription factors regulating expression of RBMXL3 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset.
	JASPAR Predicted Mouse Transcription Factor Targets 2025	transcription factors regulating expression of RBMXL3 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Mouse Transcription Factor Targets 2025 dataset.
	JASPAR Predicted Transcription Factor Targets	transcription factors regulating expression of RBMXL3 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Transcription Factor Targets dataset.
	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	cell lines with high or low copy number of RBMXL3 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset.
	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles	cell lines with RBMXL3 gene mutations from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles dataset.
	KnockTF Gene Expression Profiles with Transcription Factor Perturbations	transcription factor perturbations changing expression of RBMXL3 gene from the KnockTF Gene Expression Profiles with Transcription Factor Perturbations dataset.
	LOCATE Predicted Protein Localization Annotations	cellular components predicted to contain RBMXL3 protein from the LOCATE Predicted Protein Localization Annotations dataset.
	MotifMap Predicted Transcription Factor Targets	transcription factors regulating expression of RBMXL3 gene predicted using known transcription factor binding site motifs from the MotifMap Predicted Transcription Factor Targets dataset.
	Pathway Commons Protein-Protein Interactions	interacting proteins for RBMXL3 from the Pathway Commons Protein-Protein Interactions dataset.
	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	gene perturbations changing expression of RBMXL3 gene from the PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations dataset.
	PFOCR Pathway Figure Associations 2023	pathways involving RBMXL3 protein from the PFOCR Pathway Figure Associations 2023 dataset.
	PFOCR Pathway Figure Associations 2024	pathways involving RBMXL3 protein from the Wikipathways PFOCR 2024 dataset.
	Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles	cell types and tissues with high or low DNA methylation of RBMXL3 gene relative to other cell types and tissues from the Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles dataset.
	Roadmap Epigenomics Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at RBMXL3 gene from the Roadmap Epigenomics Histone Modification Site Profiles dataset.
	Rummagene Transcription Factor Associations 2026	transcription factors regulating expression of RBMXL3 gene from the Rummagene Transcription Factor Associations 2026 dataset.
	RummaGEO Drug Perturbation Signatures	drug perturbations changing expression of RBMXL3 gene from the RummaGEO Drug Perturbation Signatures dataset.
	RummaGEO Gene Perturbation Signatures	gene perturbations changing expression of RBMXL3 gene from the RummaGEO Gene Perturbation Signatures dataset.
	TargetScan Predicted Nonconserved microRNA Targets	microRNAs regulating expression of RBMXL3 gene predicted using nonconserved miRNA seed sequences from the TargetScan Predicted Nonconserved microRNA Targets dataset.
	TCGA Signatures of Differentially Expressed Genes for Tumors	tissue samples with high or low expression of RBMXL3 gene relative to other tissue samples from the TCGA Signatures of Differentially Expressed Genes for Tumors dataset.
	TISSUES Curated Tissue Protein Expression Evidence Scores	tissues with high expression of RBMXL3 protein from the TISSUES Curated Tissue Protein Expression Evidence Scores dataset.
	TISSUES Curated Tissue Protein Expression Evidence Scores 2025	tissues with high expression of RBMXL3 protein from the TISSUES Curated Tissue Protein Expression Evidence Scores 2025 dataset.
	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	tissues with high expression of RBMXL3 protein in proteomics datasets from the TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 dataset.
	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	tissues co-occuring with RBMXL3 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset.