| HGNC Family | PRAME family (PRAMEF) |
| Name | PRAME family member 11 |
| Description | Predicted to enable ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be part of Cul2-RING ubiquitin ligase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Mar 2025] |
| Summary |
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nAlthough none of the provided abstracts describe any role for PRAMEF11, the collection focuses extensively on the functions of the RFX3 transcription factor in mammalian development. In several studies, RFX3 is shown to be indispensable for proper ciliogenesis—ensuring that specialized monocilia, such as those present in the embryonic node for left–right (LR) axis determination, achieve their full length and functionality. For example, RFX3‐deficient mice exhibit stunted nodal cilia, resulting in laterality defects and high embryonic lethality."}, {"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 central nervous system, RFX3 contributes to the differentiation and function of ciliated cells. Its loss leads not only to hydrocephalus due to impaired differentiation of ependymal cells, but also to structural malformations such as agenesis of the corpus callosum, where mispatterned guidepost neurons disrupt proper axon pathfinding."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nRFX3 also plays a critical role in other organ systems. In the pancreas, RFX3 is expressed from early endocrine progenitors to mature islet cells, and its deficiency results in ciliary abnormalities that correlate with altered islet cellular composition, reduced insulin production, and ultimately impaired glucose tolerance."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": " Moreover, in cultured primary brain cells, RFX3 is necessary for the biogenesis and motile function of cilia and regulates the expression of key actors such as FOXJ1 and axonemal dyneins."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAdditional layers of regulation for RFX3 have been uncovered. Chromatin remodeling via histone H2B monoubiquitination (H2Bub1) has been shown to control tissue‐specific expression of cilia genes by acting at the Rfx3 locus; disruption of this process leads to defects in cilia motility and aberrant cardiac laterality, linking chromatin regulation with ciliary function."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": " Compounding these molecular interactions, a microRNA—miR‑342‑3p—has been found to directly bind the 3′‑UTR of Rfx3, downregulating its expression and, when perturbed, contributing to insulin resistance and abnormal liver gluconeogenesis in gestational diabetes mellitus models."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nOther studies broaden the context by showing that RFX transcription factors, including RFX3, act redundantly as well as in a gene‐specific manner to orchestrate the transcriptional programs required for proper cilia assembly in a variety of cell types, including ependymal and multiciliated epithelial cells."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "9"}]}, {"type": "t", "text": " Separately, detailed investigation of RFX family members in spermatogenesis has confirmed a predominant role for RFX2 and a limited prevalence of full‐length RFX4 protein, reinforcing the concept that RFX3 (and its related family members) is a pivotal regulator in multiple developmental contexts."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "10"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIt is important to note that one abstract examined endoplasmic reticulum stress in retinal vascular degeneration without providing insights into RFX3 or ciliary functions."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "11"}]}, {"type": "t", "text": " Likewise, studies on the formation of corticothalamic/thalamocortical tracts in Rfx3 mutants further emphasize the role of primary cilia in establishing the proper cellular environment necessary for neural connectivity."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "12"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn summary, while there is no information on PRAMEF11 in these abstracts, they collectively delineate RFX3 as a master transcriptional regulator essential for ciliogenesis and cilia-based signaling in various tissues—including the node, brain, and pancreas—with wide-ranging implications for developmental patterning, neural connectivity, and metabolic regulation.\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "E Bonnafe, M Touka, A AitLounis, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The transcription factor RFX3 directs nodal cilium development and left-right asymmetry specification."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.24.10.4417-4427.2004"}], "href": "https://doi.org/10.1128/MCB.24.10.4417-4427.2004"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15121860"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15121860"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "D Baas, A Meiniel, C Benadiba, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A deficiency in RFX3 causes hydrocephalus associated with abnormal differentiation of ependymal cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Eur J Neurosci (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/j.1460-9568.2006.05002.x"}], "href": "https://doi.org/10.1111/j.1460-9568.2006.05002.x"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16930429"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16930429"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Carine Benadiba, Dario Magnani, Mathieu Niquille, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The ciliogenic transcription factor RFX3 regulates early midline distribution of guidepost neurons required for corpus callosum development."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS Genet (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pgen.1002606"}], "href": "https://doi.org/10.1371/journal.pgen.1002606"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22479201"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22479201"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Aouatef Ait-Lounis, Dominique Baas, Emmanuèle Barras, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Novel function of the ciliogenic transcription factor RFX3 in development of the endocrine pancreas."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Diabetes (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.2337/db06-1187"}], "href": "https://doi.org/10.2337/db06-1187"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17229940"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17229940"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Aouatef Ait-Lounis, Claire Bonal, Queralt Seguín-Estévez, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The transcription factor Rfx3 regulates beta-cell differentiation, function, and glucokinase expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Diabetes (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.2337/db09-0986"}], "href": "https://doi.org/10.2337/db09-0986"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20413507"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20413507"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Loubna El Zein, Aouatef Ait-Lounis, Laurette Morlé, et al. "}, {"type": "b", "children": [{"type": "t", "text": "RFX3 governs growth and beating efficiency of motile cilia in mouse and controls the expression of genes involved in human ciliopathies."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Sci (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/jcs.048348"}], "href": "https://doi.org/10.1242/jcs.048348"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19671664"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19671664"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Andrew Robson, Svetlana Z Makova, Syndi Barish, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1808341116"}], "href": "https://doi.org/10.1073/pnas.1808341116"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31235600"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31235600"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Yanlan Sun, Zhou Yu, Yulei Zhang, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "The ciliogenic transcription factor Rfx3 is required for the formation of the thalamocortical tract by regulating the patterning of prethalamus and ventral telencephalon."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Mol Genet (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/hmg/ddv021"}], "href": "https://doi.org/10.1093/hmg/ddv021"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25631876"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25631876"}]}]}]}
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| Proteins | PRA11_HUMAN |
| NCBI Gene ID | 440560 |
| API | |
| Download Associations | |
| Predicted Functions |
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| Co-expressed Genes |
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| Expression in Tissues and Cell Lines |
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PRAMEF11 has 1,446 functional associations with biological entities spanning 7 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, cell line, cell type or tissue, gene, protein or microRNA) extracted from 43 datasets.
Click the + buttons to view associations for PRAMEF11 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 PRAMEF11 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset. | |
| BioGPS Cell Line Gene Expression Profiles | cell lines with high or low expression of PRAMEF11 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 PRAMEF11 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 PRAMEF11 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 PRAMEF11 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset. | |
| ChEA Transcription Factor Targets 2022 | transcription factors binding the promoter of PRAMEF11 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 PRAMEF11 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset. | |
| COMPARTMENTS Curated Protein Localization Evidence Scores 2025 | cellular components containing PRAMEF11 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset. | |
| COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 | cellular components co-occuring with PRAMEF11 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 PRAMEF11 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset. | |
| COSMIC Cell Line Gene Mutation Profiles | cell lines with PRAMEF11 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset. | |
| CTD Gene-Chemical Interactions | chemicals interacting with PRAMEF11 gene/protein from the curated CTD Gene-Chemical Interactions dataset. | |
| DepMap CRISPR Gene Dependency | cell lines with fitness changed by PRAMEF11 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 PRAMEF11 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 PRAMEF11 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 PRAMEF11 gene from the ENCODE Transcription Factor Binding Site Profiles dataset. | |
| ENCODE Transcription Factor Targets | transcription factors binding the promoter of PRAMEF11 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset. | |
| GEO Signatures of Differentially Expressed Genes for Diseases | disease perturbations changing expression of PRAMEF11 gene from the GEO Signatures of Differentially Expressed Genes for Diseases dataset. | |
| GEO Signatures of Differentially Expressed Genes for Gene Perturbations | gene perturbations changing expression of PRAMEF11 gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset. | |
| GEO Signatures of Differentially Expressed Genes for Kinase Perturbations | kinase perturbations changing expression of PRAMEF11 gene from the GEO Signatures of Differentially Expressed Genes for Kinase Perturbations dataset. | |
| GEO Signatures of Differentially Expressed Genes for Small Molecules | small molecule perturbations changing expression of PRAMEF11 gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset. | |
| GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations | transcription factor perturbations changing expression of PRAMEF11 gene from the GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations dataset. | |
| GEO Signatures of Differentially Expressed Genes for Viral Infections | virus perturbations changing expression of PRAMEF11 gene from the GEO Signatures of Differentially Expressed Genes for Viral Infections dataset. | |
| GO Biological Process Annotations 2025 | biological processes involving PRAMEF11 gene from the curated GO Biological Process Annotations2025 dataset. | |
| GO Cellular Component Annotations 2025 | cellular components containing PRAMEF11 protein from the curated GO Cellular Component Annotations 2025 dataset. | |
| GO Molecular Function Annotations 2025 | molecular functions performed by PRAMEF11 gene from the curated GO Molecular Function Annotations 2025 dataset. | |
| GTEx Tissue Gene Expression Profiles | tissues with high or low expression of PRAMEF11 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 PRAMEF11 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset. | |
| GWAS Catalog SNP-Phenotype Associations 2025 | phenotypes associated with PRAMEF11 gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset. | |
| Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles | cell lines with high or low expression of PRAMEF11 gene relative to other cell lines from the Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles dataset. | |
| JASPAR Predicted Human Transcription Factor Targets 2025 | transcription factors regulating expression of PRAMEF11 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset. | |
| JASPAR Predicted Transcription Factor Targets | transcription factors regulating expression of PRAMEF11 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 PRAMEF11 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset. | |
| KnockTF Gene Expression Profiles with Transcription Factor Perturbations | transcription factor perturbations changing expression of PRAMEF11 gene from the KnockTF Gene Expression Profiles with Transcription Factor Perturbations dataset. | |
| LINCS L1000 CMAP Chemical Perturbation Consensus Signatures | small molecule perturbations changing expression of PRAMEF11 gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset. | |
| LOCATE Predicted Protein Localization Annotations | cellular components predicted to contain PRAMEF11 protein from the LOCATE Predicted Protein Localization Annotations dataset. | |
| NIBR DRUG-seq U2OS MoA Box Gene Expression Profiles | drug perturbations changing expression of PRAMEF11 gene from the NIBR DRUG-seq U2OS MoA Box dataset. | |
| Roadmap Epigenomics Histone Modification Site Profiles | histone modification site profiles with high histone modification abundance at PRAMEF11 gene from the Roadmap Epigenomics Histone Modification Site Profiles dataset. | |
| RummaGEO Drug Perturbation Signatures | drug perturbations changing expression of PRAMEF11 gene from the RummaGEO Drug Perturbation Signatures dataset. | |
| RummaGEO Gene Perturbation Signatures | gene perturbations changing expression of PRAMEF11 gene from the RummaGEO Gene Perturbation Signatures dataset. | |
| TargetScan Predicted Nonconserved microRNA Targets | microRNAs regulating expression of PRAMEF11 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 PRAMEF11 gene relative to other tissue samples from the TCGA Signatures of Differentially Expressed Genes for Tumors dataset. | |
| TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 | tissues co-occuring with PRAMEF11 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset. | |