| HGNC Family | Basic helix-loop-helix proteins (BHLH) |
| Name | Fer3-like bHLH transcription factor |
| Description | Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in developmental process; negative regulation of DNA-templated transcription; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including floor plate development; regulation of dopaminergic neuron differentiation; and regulation of neurogenesis. Predicted to be located in chromatin and nucleus. [provided by Alliance of Genome Resources, Mar 2025] |
| Summary |
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n FERD3L, also known as Nato3, is a member of the basic helix‐loop‐helix transcription factor family that plays a critical role in neural development. In several studies its expression has been shown to be directly induced by the transcription factor Foxa2 and integrated within signaling cascades (including Sonic hedgehog) to promote the specification and differentiation of floor plate cells and midbrain dopaminergic neurons (see."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": " Functional studies in chick, mouse, and Drosophila models have demonstrated that Nato3/FERD3L is essential for maintaining the neurogenic potential of floor plate cells and for driving dopaminergic progenitor gene networks; its loss leads to defects including impaired differentiation, mitochondrial abnormalities, and subsequent locomotor impairments that model aspects of neurodegeneration (see."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}, {"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In addition to its well‐characterized role in neural development, alterations in FERD3L expression have been observed in vascular disease contexts. For example, even though risk alleles at nearby loci such as HDAC9 and TWIST1 may modulate vascular pathology, FERD3L expression appears less affected in these settings; lower messenger RNA levels in patient samples have been reported in studies of ischemic stroke and intracranial aneurysms (see."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Furthermore, genomic deletions encompassing FERD3L—as observed in patients with Saethre‐Chotzen syndrome accompanied by intellectual disability and craniofacial abnormalities—suggest that FERD3L may contribute to broader developmental processes beyond the central nervous system (see."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In summary, cumulative evidence indicates that FERD3L/Nato3 is a key transcriptional regulator that orchestrates neural progenitor identity and mediates the proper maturation of dopaminergic neurons. Its function is crucial during early neural development and the maintenance of dopaminergic circuitry, with potential implications in neurodegeneration as well as in vascular and craniofacial developmental disorders.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Emmanouil Metzakopian, Wei Lin, Mali Salmon-Divon, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Development (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/dev.081034"}], "href": "https://doi.org/10.1242/dev.081034"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22696295"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22696295"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Abed AlFatah Mansour, Einat Nissim-Eliraz, Sophie Zisman, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Foxa2 regulates the expression of Nato3 in the floor plate by a novel evolutionarily conserved promoter."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Neurosci (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.mcn.2010.09.002"}], "href": "https://doi.org/10.1016/j.mcn.2010.09.002"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20849957"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20849957"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Doug J Peterson, Darcy N Marckini, Jordan L Straight, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The Basic Helix-Loop-Helix Gene Nato3 Drives Expression of Dopaminergic Neuron Transcription Factors in Neural Progenitors."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Neuroscience (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.neuroscience.2019.09.003"}], "href": "https://doi.org/10.1016/j.neuroscience.2019.09.003"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31672641"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31672641"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Emmanouil Metzakopian, Kamal Bouhali, Matías Alvarez-Saavedra, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Genome-wide characterisation of Foxa1 binding sites reveals several mechanisms for regulating neuronal differentiation in midbrain dopamine cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Development (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/dev.115808"}], "href": "https://doi.org/10.1242/dev.115808"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25804738"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25804738"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Federico Miozzo, Eva P Valencia-Alarcón, Luca Stickley, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Maintenance of mitochondrial integrity in midbrain dopaminergic neurons governed by a conserved developmental transcription factor."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41467-022-29075-0"}], "href": "https://doi.org/10.1038/s41467-022-29075-0"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "35301315"}], "href": "https://pubmed.ncbi.nlm.nih.gov/35301315"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Silvia Ferronato, Matteo Gelati, Alberto Scuro, et al. "}, {"type": "b", "children": [{"type": "t", "text": "HDAC9, TWIST1 and FERD3L gene expression in asymptomatic stable and unstable carotid plaques."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Inflamm Res (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00011-015-0904-z"}], "href": "https://doi.org/10.1007/s00011-015-0904-z"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26621503"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26621503"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Shu Chai Ching, Lim Jing Wen, Nor Ismaliza Mohd Ismail, et al. "}, {"type": "b", "children": [{"type": "t", "text": "SLC17A3 rs9379800 and Ischemic Stroke Susceptibility at the Northern Region of Malaysia."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Stroke Cerebrovasc Dis (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jstrokecerebrovasdis.2021.105908"}], "href": "https://doi.org/10.1016/j.jstrokecerebrovasdis.2021.105908"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "34384670"}], "href": "https://pubmed.ncbi.nlm.nih.gov/34384670"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Hiroko Shimbo, Tatsuki Oyoshi, Kenji Kurosawa "}, {"type": "b", "children": [{"type": "t", "text": "Contiguous gene deletion neighboring TWIST1 identified in a patient with Saethre-Chotzen syndrome associated with neurodevelopmental delay: Possible contribution of HDAC9."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Congenit Anom (Kyoto) (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/cga.12216"}], "href": "https://doi.org/10.1111/cga.12216"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28220539"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28220539"}]}]}]}
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| Synonyms | PTFB, N-TWIST, BHLHA31, NTWIST, NATO3 |
| Proteins | FER3L_HUMAN |
| NCBI Gene ID | 222894 |
| 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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FERD3L has 1,902 functional associations with biological entities spanning 8 categories (molecular profile, organism, functional term, phrase or reference, disease, phenotype or trait, chemical, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 71 datasets.
Click the + buttons to view associations for FERD3L from the datasets below.
If available, associations are ranked by standardized value
| Dataset | Summary | |
|---|---|---|
| Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles | tissues with high or low expression of FERD3L 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 FERD3L 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 FERD3L 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 FERD3L 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 FERD3L 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 FERD3L 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 FERD3L gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset. | |
| CCLE Cell Line Gene CNV Profiles | cell lines with high or low copy number of FERD3L 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 FERD3L gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset. | |
| ChEA Transcription Factor Binding Site Profiles | transcription factor binding site profiles with transcription factor binding evidence at the promoter of FERD3L gene from the CHEA Transcription Factor Binding Site Profiles dataset. | |
| ChEA Transcription Factor Targets | transcription factors binding the promoter of FERD3L 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 FERD3L 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 FERD3L gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset. | |
| COMPARTMENTS Curated Protein Localization Evidence Scores | cellular components containing FERD3L protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset. | |
| COMPARTMENTS Curated Protein Localization Evidence Scores 2025 | cellular components containing FERD3L protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset. | |
| COMPARTMENTS Text-mining Protein Localization Evidence Scores | cellular components co-occuring with FERD3L 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 FERD3L 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 FERD3L gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset. | |
| COSMIC Cell Line Gene Mutation Profiles | cell lines with FERD3L gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset. | |
| CTD Gene-Disease Associations | diseases associated with FERD3L gene/protein from the curated CTD Gene-Disease Associations dataset. | |
| DepMap CRISPR Gene Dependency | cell lines with fitness changed by FERD3L 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 FERD3L 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 FERD3L 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 FERD3L 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 FERD3L gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset. | |
| ENCODE Histone Modification Site Profiles | histone modification site profiles with high histone modification abundance at FERD3L 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 FERD3L gene from the ENCODE Transcription Factor Binding Site Profiles dataset. | |
| ENCODE Transcription Factor Targets | transcription factors binding the promoter of FERD3L 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 FERD3L from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset. | |
| GAD High Level Gene-Disease Associations | diseases associated with FERD3L gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset. | |
| GeneRIF Biological Term Annotations | biological terms co-occuring with FERD3L gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset. | |
| GeneSigDB Published Gene Signatures | PubMedIDs of publications reporting gene signatures containing FERD3L from the GeneSigDB Published Gene Signatures dataset. | |
| GEO Signatures of Differentially Expressed Genes for Diseases | disease perturbations changing expression of FERD3L 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 FERD3L 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 FERD3L 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 FERD3L 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 FERD3L gene from the GEO Signatures of Differentially Expressed Genes for Viral Infections dataset. | |
| GO Biological Process Annotations 2015 | biological processes involving FERD3L gene from the curated GO Biological Process Annotations 2015 dataset. | |
| GO Biological Process Annotations 2023 | biological processes involving FERD3L gene from the curated GO Biological Process Annotations 2023 dataset. | |
| GO Biological Process Annotations 2025 | biological processes involving FERD3L gene from the curated GO Biological Process Annotations2025 dataset. | |
| GO Cellular Component Annotations 2015 | cellular components containing FERD3L protein from the curated GO Cellular Component Annotations 2015 dataset. | |
| GO Cellular Component Annotations 2023 | cellular components containing FERD3L protein from the curated GO Cellular Component Annotations 2023 dataset. | |
| GO Cellular Component Annotations 2025 | cellular components containing FERD3L protein from the curated GO Cellular Component Annotations 2025 dataset. | |
| GO Molecular Function Annotations 2015 | molecular functions performed by FERD3L gene from the curated GO Molecular Function Annotations 2015 dataset. | |
| GO Molecular Function Annotations 2023 | molecular functions performed by FERD3L gene from the curated GO Molecular Function Annotations 2023 dataset. | |
| GO Molecular Function Annotations 2025 | molecular functions performed by FERD3L gene from the curated GO Molecular Function Annotations 2025 dataset. | |
| GTEx Tissue Gene Expression Profiles | tissues with high or low expression of FERD3L gene relative to other tissues from the GTEx Tissue Gene Expression Profiles dataset. | |
| GWAS Catalog SNP-Phenotype Associations 2025 | phenotypes associated with FERD3L 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 FERD3L gene relative to other cell lines from the Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles dataset. | |
| HPA Tissue Protein Expression Profiles | tissues with high or low expression of FERD3L protein relative to other tissues from the HPA Tissue Protein Expression Profiles dataset. | |
| InterPro Predicted Protein Domain Annotations | protein domains predicted for FERD3L protein from the InterPro Predicted Protein Domain Annotations dataset. | |
| JASPAR Predicted Human Transcription Factor Targets 2025 | transcription factors regulating expression of FERD3L 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 FERD3L 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 FERD3L 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 FERD3L 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 FERD3L gene from the KnockTF Gene Expression Profiles with Transcription Factor Perturbations dataset. | |
| LOCATE Predicted Protein Localization Annotations | cellular components predicted to contain FERD3L protein from the LOCATE Predicted Protein Localization Annotations dataset. | |
| MGI Mouse Phenotype Associations 2023 | phenotypes of transgenic mice caused by FERD3L gene mutations from the MGI Mouse Phenotype Associations 2023 dataset. | |
| MotifMap Predicted Transcription Factor Targets | transcription factors regulating expression of FERD3L gene predicted using known transcription factor binding site motifs from the MotifMap Predicted Transcription Factor Targets dataset. | |
| MPO Gene-Phenotype Associations | phenotypes of transgenic mice caused by FERD3L gene mutations from the MPO Gene-Phenotype Associations dataset. | |
| MSigDB Signatures of Differentially Expressed Genes for Cancer Gene Perturbations | gene perturbations changing expression of FERD3L gene from the MSigDB Signatures of Differentially Expressed Genes for Cancer Gene Perturbations dataset. | |
| Pathway Commons Protein-Protein Interactions | interacting proteins for FERD3L from the Pathway Commons Protein-Protein Interactions dataset. | |
| Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles | cell types and tissues with high or low DNA methylation of FERD3L 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 FERD3L gene from the Roadmap Epigenomics Histone Modification Site Profiles dataset. | |
| Rummagene Transcription Factor Associations 2026 | transcription factors regulating expression of FERD3L gene from the Rummagene Transcription Factor Associations 2026 dataset. | |
| RummaGEO Drug Perturbation Signatures | drug perturbations changing expression of FERD3L gene from the RummaGEO Drug Perturbation Signatures dataset. | |
| RummaGEO Gene Perturbation Signatures | gene perturbations changing expression of FERD3L gene from the RummaGEO Gene Perturbation Signatures dataset. | |
| TCGA Signatures of Differentially Expressed Genes for Tumors | tissue samples with high or low expression of FERD3L 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 | tissues co-occuring with FERD3L protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores dataset. | |
| TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 | tissues co-occuring with FERD3L protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset. | |
| WikiPathways Pathways 2024 | pathways involving FERD3L protein from the WikiPathways Pathways 2024 dataset. | |
