| Name | KH domain containing 4, pre-mRNA splicing factor |
| Description | Enables RNA binding activity. Involved in mRNA splice site recognition. Located in cytoplasm; nucleoplasm; and spliceosomal complex. [provided by Alliance of Genome Resources, Mar 2025] |
| Summary |
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n Recent research on competing endogenous RNA (ceRNA) networks in cancer has revealed that noncoding RNA‐mediated regulation plays a pivotal role in controlling gene expression and tumor cell behavior. In a study of breast cancer, the long noncoding RNA LINC00665 was shown to promote cell survival and metastasis by “sponging” miR‑641, which in turn targets several mRNAs. Among these potential downstream targets, KHDC4 was identified by quantitative PCR alongside other candidates (e.g., SRCAP, SIKE1, NADK, and HSPG2)."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": " Although further functional validation was performed for SRCAP – establishing its role in counteracting the antiproliferative and anti‑invasive effects induced by miR‑641 – KHDC4’s inclusion as a putative target suggests that it may also participate in the regulation of oncogenic pathways in breast cancer. \n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Notably, KHDC4 belongs to the family of KH domain‐containing proteins, which are well documented for their roles in RNA binding and the regulation of pre‑mRNA processing events such as splicing."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": " This connection reinforces the possibility that KHDC4 might contribute to fine‑tuning post‑transcriptional gene regulation in neoplastic cells. Furthermore, the broader landscape of noncoding RNA research demonstrates that deregulated RNA networks—including those involving small nucleolar RNAs and circular RNAs—can modulate diverse cancer cell functions, from proliferation to invasion."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": " \n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In summary, although the direct functional consequences of KHDC4 modulation in breast cancer remain to be fully elucidated, its identification as a candidate target within a miR‑641–mediated ceRNA regulatory axis positions KHDC4 as a promising subject for further investigation. Clarifying its role may not only extend our understanding of RNA‑binding protein function in cancer but also eventually contribute to the development of novel prognostic biomarkers or therapeutic targets.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Wen Cao, Xiaojing Liu, Weijia Su, et al. "}, {"type": "b", "children": [{"type": "t", "text": "LINC00665 sponges miR-641 to promote the progression of breast cancer by targeting the SNF2-related CREBBP activator protein (SRCAP)."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Bioengineered (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1080/21655979.2022.2031402"}], "href": "https://doi.org/10.1080/21655979.2022.2031402"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "35152838"}], "href": "https://pubmed.ncbi.nlm.nih.gov/35152838"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Marlies Löscher, Markus Schosserer, Eric Dausse, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Inhibition of pre-mRNA splicing by a synthetic Blom7α-interacting small RNA."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS One (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pone.0047497"}], "href": "https://doi.org/10.1371/journal.pone.0047497"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23144703"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23144703"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Kaiissar Mannoor, Jipei Liao, Feng Jiang "}, {"type": "b", "children": [{"type": "t", "text": "Small nucleolar RNAs in cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochim Biophys Acta (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbcan.2012.03.005"}], "href": "https://doi.org/10.1016/j.bbcan.2012.03.005"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22498252"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22498252"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "L S Kristensen, T B Hansen, M T Venø, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Circular RNAs in cancer: opportunities and challenges in the field."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Oncogene (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/onc.2017.361"}], "href": "https://doi.org/10.1038/onc.2017.361"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28991235"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28991235"}]}]}]}
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| NCBI Gene ID | 22889 |
| 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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KHDC4 has 2,893 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 39 datasets.
Click the + buttons to view associations for KHDC4 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 KHDC4 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 KHDC4 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset. | |
| CCLE Cell Line Proteomics | Cell lines associated with KHDC4 protein from the CCLE Cell Line Proteomics dataset. | |
| CellMarker Gene-Cell Type Associations | cell types associated with KHDC4 gene from the CellMarker Gene-Cell Type Associations dataset. | |
| ChEA Transcription Factor Targets 2022 | transcription factors binding the promoter of KHDC4 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 KHDC4 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset. | |
| COMPARTMENTS Curated Protein Localization Evidence Scores 2025 | cellular components containing KHDC4 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset. | |
| COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 | cellular components containing KHDC4 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 KHDC4 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 KHDC4 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 KHDC4 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 KHDC4 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 KHDC4 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 KHDC4 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset. | |
| GO Biological Process Annotations 2023 | biological processes involving KHDC4 gene from the curated GO Biological Process Annotations 2023 dataset. | |
| GO Biological Process Annotations 2025 | biological processes involving KHDC4 gene from the curated GO Biological Process Annotations2025 dataset. | |
| GO Cellular Component Annotations 2023 | cellular components containing KHDC4 protein from the curated GO Cellular Component Annotations 2023 dataset. | |
| GO Cellular Component Annotations 2025 | cellular components containing KHDC4 protein from the curated GO Cellular Component Annotations 2025 dataset. | |
| GO Molecular Function Annotations 2023 | molecular functions performed by KHDC4 gene from the curated GO Molecular Function Annotations 2023 dataset. | |
| GTEx Tissue Gene Expression Profiles 2023 | tissues with high or low expression of KHDC4 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 KHDC4 gene relative to other tissue samples from the GTEx Tissue-Specific Aging Signatures dataset. | |
| GWAS Catalog SNP-Phenotype Associations 2025 | phenotypes associated with KHDC4 gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset. | |
| JASPAR Predicted Human Transcription Factor Targets 2025 | transcription factors regulating expression of KHDC4 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 KHDC4 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 KHDC4 gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset. | |
| LINCS L1000 CMAP CRISPR Knockout Consensus Signatures | gene perturbations changing expression of KHDC4 gene from the LINCS L1000 CMAP CRISPR Knockout Consensus Signatures dataset. | |
| MoTrPAC Rat Endurance Exercise Training | tissue samples with high or low expression of KHDC4 gene relative to other tissue samples from the MoTrPAC Rat Endurance Exercise Training dataset. | |
| NIBR DRUG-seq U2OS MoA Box Gene Expression Profiles | drug perturbations changing expression of KHDC4 gene from the NIBR DRUG-seq U2OS MoA Box dataset. | |
| Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures | gene perturbations changing expression of KHDC4 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 KHDC4 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 KHDC4 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 KHDC4 gene from the Rummagene Transcription Factor Associations 2026 dataset. | |
| RummaGEO Drug Perturbation Signatures | drug perturbations changing expression of KHDC4 gene from the RummaGEO Drug Perturbation Signatures dataset. | |
| RummaGEO Gene Perturbation Signatures | gene perturbations changing expression of KHDC4 gene from the RummaGEO Gene Perturbation Signatures dataset. | |
| Sci-Plex Drug Perturbation Signatures | drug perturbations changing expression of KHDC4 gene from the Sci-Plex Drug Perturbation Signatures dataset. | |
| Tahoe Therapeutics Tahoe 100M Perturbation Atlas | drug perturbations changing expression of KHDC4 gene from the Tahoe Therapeutics Tahoe 100M Perturbation Atlas dataset. | |
| TISSUES Curated Tissue Protein Expression Evidence Scores 2025 | tissues with high expression of KHDC4 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 KHDC4 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 KHDC4 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset. | |