MIR9-3 Gene

HGNC Family Non-coding RNAs
Name microRNA 9-3
Description microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nStudies in the developing brain have revealed critical roles for MIR9‐3 in neural differentiation and synaptic plasticity. In mouse telencephalon, combined inactivation of the MIR9‐2 and MIR9‐3 loci results in dysregulation of key transcription factors—including elevated Foxg1 levels—and alters the balance between progenitor proliferation and neuronal differentiation, causing defects in cortical layering and interneuron migration. In parallel, selective inhibition of the MIR9‐3–derived miR‐9‑3p in the hippocampus impairs long‐term potentiation and hippocampus‐dependent memory, highlighting its importance in modulating synaptic plasticity."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn several human cancers, epigenetic silencing of MIR9‐3 via promoter hypermethylation has been implicated in tumor development and progression. In clear cell renal cell carcinoma, hypermethylation of both MIR9‐1 and MIR9‐3 is associated with decreased microRNA expression and a markedly increased risk of metastatic recurrence. Similar methylation‐mediated inactivation of MIR9–encoding loci, including MIR9‐3, is observed in gastric cancer and cervical adenocarcinoma, where loss of its tumor‐suppressive function leads to enhanced cell proliferation, migration, and invasion. In non‐small cell lung cancer, both promoter methylation of MIR9‐3 and its reduced expression are linked with advanced tumor stage, and sulforaphane treatment has been shown to restore MIR9‐3 levels through epigenetic modifications. Further, decreased MIR9‐3–derived miR‐9‑3p in nasopharyngeal carcinoma correlates with deregulation of extracellular matrix components and activation of epithelial–mesenchymal transition, while in glioma a reduction in miR‐9‑3p contributes to increased Herpud1 expression, thereby protecting tumor cells against apoptosis. Finally, aberrant methylation of MIR9 family genes—including MIR9‐3—is also suggested in multiple myeloma, further supporting its role as a tumor suppressor across diverse malignancies."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "3", "end_ref": "11"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAdditional regulatory mechanisms may further modulate MIR9‐3 function in cancer. In hepatocellular carcinoma, for example, the long noncoding RNA SAMMSON downregulates miR‐9‑3p, thereby promoting cancer cell migration and invasion and contributing to a more aggressive phenotype."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "12"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Mikihito Shibata, Hiromi Nakao, Hiroshi Kiyonari, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Elevation of MiR-9-3p suppresses the epithelial-mesenchymal transition of nasopharyngeal carcinoma cells via down-regulating FN1, ITGB1 and ITGAV."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cancer Biol Ther (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1080/15384047.2017.1323585"}], "href": "https://doi.org/10.1080/15384047.2017.1323585"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28613134"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28613134"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Ling Yang, Yongping Mu, Hongwei Cui, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Infrequent DNA methylation of miR-9-1 and miR-9-3 in multiple myeloma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Clin Pathol (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1136/jclinpath-2014-202817"}], "href": "https://doi.org/10.1136/jclinpath-2014-202817"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25855800"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25855800"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Shouzhang Yang, Huajie Cai, Bingren Hu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "LncRNA SAMMSON negatively regulates miR-9-3p in hepatocellular carcinoma cells and has prognostic values."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biosci Rep (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1042/BSR20190615"}], "href": "https://doi.org/10.1042/BSR20190615"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31164410"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31164410"}]}]}]}
Synonyms HSA-MIR-9-3, MIRN9-3, MIR-9-3, MIRNA9-3
NCBI Gene ID 407051
API
Download Associations
Predicted Functions View MIR9-3's ARCHS4 Predicted Functions.
Co-expressed Genes View MIR9-3's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View MIR9-3's ARCHS4 Predicted Functions.

Functional Associations

MIR9-3 has 659 functional associations with biological entities spanning 6 categories (molecular profile, chemical, functional term, phrase or reference, disease, phenotype or trait, cell line, cell type or tissue, gene, protein or microRNA) extracted from 23 datasets.

Click the + buttons to view associations for MIR9-3 from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
CCLE Cell Line Gene CNV Profiles cell lines with high or low copy number of MIR9-3 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
ChEA Transcription Factor Binding Site Profiles transcription factor binding site profiles with transcription factor binding evidence at the promoter of MIR9-3 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
ChEA Transcription Factor Targets transcription factors binding the promoter of MIR9-3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
COSMIC Cell Line Gene CNV Profiles cell lines with high or low copy number of MIR9-3 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
CTD Gene-Chemical Interactions chemicals interacting with MIR9-3 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
ENCODE Histone Modification Site Profiles histone modification site profiles with high histone modification abundance at MIR9-3 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 MIR9-3 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
ENCODE Transcription Factor Targets transcription factors binding the promoter of MIR9-3 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 MIR9-3 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
GAD Gene-Disease Associations diseases associated with MIR9-3 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
GeneRIF Biological Term Annotations biological terms co-occuring with MIR9-3 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
GEO Signatures of Differentially Expressed Genes for Gene Perturbations gene perturbations changing expression of MIR9-3 gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset.
GEO Signatures of Differentially Expressed Genes for Small Molecules small molecule perturbations changing expression of MIR9-3 gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset.
HuGE Navigator Gene-Phenotype Associations phenotypes associated with MIR9-3 gene by text-mining GWAS publications from the HuGE Navigator Gene-Phenotype Associations dataset.
JASPAR Predicted Transcription Factor Targets transcription factors regulating expression of MIR9-3 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 MIR9-3 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 MIR9-3 gene from the KnockTF Gene Expression Profiles with Transcription Factor Perturbations dataset.
MGI Mouse Phenotype Associations 2023 phenotypes of transgenic mice caused by MIR9-3 gene mutations from the MGI Mouse Phenotype Associations 2023 dataset.
MotifMap Predicted Transcription Factor Targets transcription factors regulating expression of MIR9-3 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 MIR9-3 gene mutations from the MPO Gene-Phenotype Associations dataset.
Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles cell types and tissues with high or low DNA methylation of MIR9-3 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 MIR9-3 gene from the Roadmap Epigenomics Histone Modification Site Profiles dataset.
WikiPathways Pathways 2014 pathways involving MIR9-3 protein from the Wikipathways Pathways 2014 dataset.