RTRAF Gene

Name RNA transcription, translation and transport factor
Description Enables RNA binding activity; RNA polymerase II complex binding activity; and identical protein binding activity. Involved in negative regulation of protein kinase activity; positive regulation of transcription by RNA polymerase II; and tRNA splicing, via endonucleolytic cleavage and ligation. Located in microtubule cytoskeleton; nucleoplasm; and perinuclear region of cytoplasm. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Mar 2025]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nC14orf166, also known as RTRAF or hCLE, is a multifunctional protein that plays a central role in RNA metabolism. It modulates nuclear RNA processing by interacting with RNA polymerase II, thereby influencing transcription initiation, elongation, and processing. In addition, C14orf166 is involved in nucleo‐cytoplasmic RNA transport—it shuttles between the nucleus and cytoplasm as part of RNA granule complexes containing factors such as DDX1, HSPC117, and FAM98 proteins. These activities underline its importance in regulating gene expression at multiple levels."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn the context of viral infections, C14orf166 has been shown to interact with viral proteins, thereby influencing the virus life cycle. The protein binds to the hepatitis C virus core protein—potentially impacting mRNA metabolism, gene regulation, and even microtubule organization—and to the influenza virus polymerase complex where it stimulates viral RNA transcription and replication. Notably, during influenza infection, C14orf166 is maintained or even increased despite host transcriptional shut-off, and it is found in association with viral ribonucleoproteins both in the nucleus and cytoplasm, even becoming incorporated within mature virions, suggesting a multifaceted role in facilitating efficient viral propagation."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}, {"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAberrant overexpression of C14orf166 has been documented in several human cancers, where it correlates with aggressive clinical behavior and poor patient outcomes. In pancreatic cancer, for example, higher expression levels are associated with lymph node metastasis, suggesting a role in tumor dissemination. Similarly, in cervical and nasopharyngeal carcinomas high C14orf166 expression is linked to advanced disease stage, larger tumor size, and reduced overall survival. Increased expression is also noted in bladder and breast cancers, and it appears that through its actions on transcription and RNA processing—as well as its interplay with other molecular partners (for instance, within complexes that modulate oncogenic proteins like PRMT1)—C14orf166 contributes to tumor progression and metastasis."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "5", "end_ref": "10"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Alicia Pérez-González, Alejandra Pazo, Rosana Navajas, et al. "}, {"type": "b", "children": [{"type": "t", "text": "hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel transcription-dependent shuttling RNA-transporting complex."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS One (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pone.0090957"}], "href": "https://doi.org/10.1371/journal.pone.0090957"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24608264"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24608264"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Elif Çağlayan, Kadir Turan "}, {"type": "b", "children": [{"type": "t", "text": "An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein from yeast-two-hybrid screening data."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proteins (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/prot.26534"}], "href": "https://doi.org/10.1002/prot.26534"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "37265372"}], "href": "https://pubmed.ncbi.nlm.nih.gov/37265372"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Jun-Wei Lee, Pao-Chi Liao, Kung-Chia Young, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Identification of hnRNPH1, NF45, and C14orf166 as novel host interacting partners of the mature hepatitis C virus core protein."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Proteome Res (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1021/pr200338d"}], "href": "https://doi.org/10.1021/pr200338d"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21823664"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21823664"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Ariel Rodriguez-Frandsen, Susana de Lucas, Alicia Pérez-González, et al. "}, {"type": "b", "children": [{"type": "t", "text": "hCLE/C14orf166, a cellular protein required for viral replication, is incorporated into influenza virus particles."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Rep (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/srep20744"}], "href": "https://doi.org/10.1038/srep20744"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26864902"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26864902"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Yazhou Cui, Jianmei Wu, Meijuan Zong, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Proteomic profiling in pancreatic cancer with and without lymph node metastasis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Int J Cancer (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/ijc.24163"}], "href": "https://doi.org/10.1002/ijc.24163"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19152423"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19152423"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Lin Yang, Fengyan Li, Fangyong Lei, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Overexpression of chromosome 14 open reading frame 166 correlates with disease progression and poorer prognosis in human NPC."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Tumour Biol (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s13277-015-3518-8"}], "href": "https://doi.org/10.1007/s13277-015-3518-8"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25964093"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25964093"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Weijing Zhang, Jianping Ou, Fangyong Lei, et al. "}, {"type": "b", "children": [{"type": "t", "text": "C14ORF166 overexpression is associated with pelvic lymph node metastasis and poor prognosis in uterine cervical cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Tumour Biol (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s13277-015-3806-3"}], "href": "https://doi.org/10.1007/s13277-015-3806-3"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26219895"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26219895"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Tuck-yun Cheang, Hong-Yan Zhou, Wei Chen, et al. "}, {"type": "b", "children": [{"type": "t", "text": "C14orf166 overexpression correlates with tumor progression and poor prognosis of breast cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Transl Med (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s12967-016-0805-0"}], "href": "https://doi.org/10.1186/s12967-016-0805-0"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26883017"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26883017"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Mingkun Chen, Yunlin Ye, Baojia Zou, et al. "}, {"type": "b", "children": [{"type": "t", "text": "C14orf166 is a high-risk biomarker for bladder cancer and promotes bladder cancer cell proliferation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Transl Med (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s12967-016-0801-4"}], "href": "https://doi.org/10.1186/s12967-016-0801-4"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26905879"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26905879"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Khondker Ayesha Akter, Mohammed A Mansour, Toshinori Hyodo, et al. "}, {"type": "b", "children": [{"type": "t", "text": "FAM98A associates with DDX1-C14orf166-FAM98B in a novel complex involved in colorectal cancer progression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Int J Biochem Cell Biol (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.biocel.2016.12.013"}], "href": "https://doi.org/10.1016/j.biocel.2016.12.013"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28040436"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28040436"}]}]}]}
NCBI Gene ID 51637
API
Download Associations
Predicted Functions View RTRAF's ARCHS4 Predicted Functions.
Co-expressed Genes View RTRAF's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View RTRAF's ARCHS4 Predicted Functions.

Functional Associations

RTRAF has 2,496 functional associations with biological entities spanning 5 categories (chemical, functional term, phrase or reference, disease, phenotype or trait, cell line, cell type or tissue, gene, protein or microRNA) extracted from 45 datasets.

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

If available, associations are ranked by standardized value

Dataset Summary
Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles tissue samples with high or low expression of RTRAF gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
Carcinogenome Chemical Perturbation Carcinogenicity Signatures small molecule perturbations changing expression of RTRAF gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
CCLE Cell Line Proteomics Cell lines associated with RTRAF protein from the CCLE Cell Line Proteomics dataset.
CellMarker Gene-Cell Type Associations cell types associated with RTRAF gene from the CellMarker Gene-Cell Type Associations dataset.
ChEA Transcription Factor Targets 2022 transcription factors binding the promoter of RTRAF 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 RTRAF gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
COMPARTMENTS Curated Protein Localization Evidence Scores 2025 cellular components containing RTRAF protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 cellular components containing RTRAF 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 2025 cellular components co-occuring with RTRAF protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
DeepCoverMOA Drug Mechanisms of Action small molecule perturbations with high or low expression of RTRAF 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 RTRAF 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 RTRAF gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
DISEASES Text-mining Gene-Disease Association Evidence Scores 2025 diseases co-occuring with RTRAF 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 RTRAF gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
DisGeNET Gene-Phenotype Associations phenotypes associated with RTRAF gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
GO Biological Process Annotations 2023 biological processes involving RTRAF gene from the curated GO Biological Process Annotations 2023 dataset.
GO Biological Process Annotations 2025 biological processes involving RTRAF gene from the curated GO Biological Process Annotations2025 dataset.
GO Cellular Component Annotations 2023 cellular components containing RTRAF protein from the curated GO Cellular Component Annotations 2023 dataset.
GO Cellular Component Annotations 2025 cellular components containing RTRAF protein from the curated GO Cellular Component Annotations 2025 dataset.
GO Molecular Function Annotations 2023 molecular functions performed by RTRAF gene from the curated GO Molecular Function Annotations 2023 dataset.
GO Molecular Function Annotations 2025 molecular functions performed by RTRAF gene from the curated GO Molecular Function Annotations 2025 dataset.
GTEx Tissue Gene Expression Profiles 2023 tissues with high or low expression of RTRAF gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
GTEx Tissue-Specific Aging Signatures tissue samples with high or low expression of RTRAF gene relative to other tissue samples from the GTEx Tissue-Specific Aging Signatures dataset.
GWAS Catalog SNP-Phenotype Associations 2025 phenotypes associated with RTRAF gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset.
IMPC Knockout Mouse Phenotypes phenotypes of mice caused by RTRAF gene knockout from the IMPC Knockout Mouse Phenotypes dataset.
JASPAR Predicted Human Transcription Factor Targets 2025 transcription factors regulating expression of RTRAF 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 RTRAF gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Mouse Transcription Factor Targets 2025 dataset.
LINCS L1000 CMAP Chemical Perturbation Consensus Signatures small molecule perturbations changing expression of RTRAF gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset.
LINCS L1000 CMAP CRISPR Knockout Consensus Signatures gene perturbations changing expression of RTRAF gene from the LINCS L1000 CMAP CRISPR Knockout Consensus Signatures dataset.
MGI Mouse Phenotype Associations 2023 phenotypes of transgenic mice caused by RTRAF gene mutations from the MGI Mouse Phenotype Associations 2023 dataset.
NIBR DRUG-seq U2OS MoA Box Gene Expression Profiles drug perturbations changing expression of RTRAF gene from the NIBR DRUG-seq U2OS MoA Box dataset.
PFOCR Pathway Figure Associations 2023 pathways involving RTRAF protein from the PFOCR Pathway Figure Associations 2023 dataset.
PFOCR Pathway Figure Associations 2024 pathways involving RTRAF protein from the Wikipathways PFOCR 2024 dataset.
Reactome Pathways 2024 pathways involving RTRAF protein from the Reactome Pathways 2024 dataset.
Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of RTRAF gene from the Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures dataset.
Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of RTRAF gene from the Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures dataset.
Replogle et al., Cell, 2022 RPE1 Essential Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of RTRAF gene from the Replogle et al., Cell, 2022 RPE1 Essential Perturb-seq Gene Perturbation Signatures dataset.
Rummagene Transcription Factor Associations 2026 transcription factors regulating expression of RTRAF gene from the Rummagene Transcription Factor Associations 2026 dataset.
RummaGEO Drug Perturbation Signatures drug perturbations changing expression of RTRAF gene from the RummaGEO Drug Perturbation Signatures dataset.
RummaGEO Gene Perturbation Signatures gene perturbations changing expression of RTRAF gene from the RummaGEO Gene Perturbation Signatures dataset.
Sci-Plex Drug Perturbation Signatures drug perturbations changing expression of RTRAF gene from the Sci-Plex Drug Perturbation Signatures dataset.
Tahoe Therapeutics Tahoe 100M Perturbation Atlas drug perturbations changing expression of RTRAF gene from the Tahoe Therapeutics Tahoe 100M Perturbation Atlas dataset.
TISSUES Curated Tissue Protein Expression Evidence Scores 2025 tissues with high expression of RTRAF 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 RTRAF 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 RTRAF protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset.