MIR509-3

Summary

MIR509-3 (microRNA 509-3, HGNC:33675) is a microRNA gene on chromosome Xq27.3.

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.

Source: NCBI Gene 100126337 — RefSeq curated summary.

At a glance

• Gene type: non-coding (miRNA) — no protein product; not a drug target. Variant/disease associations are omitted (they would be positional, from an overlapping protein-coding gene).

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33675
Approved symbol	MIR509-3
Name	microRNA 509-3
Location	Xq27.3
Locus type	RNA, micro
Status	Approved
Aliases	hsa-mir-509-3
Ensembl gene	ENSG00000212014
Ensembl biotype	miRNA
OMIM	300876
Entrez	100126337
RNAcentral	URS000075B370 — miRNA, 75 nt, 3 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 miRNA

ENST00000390725

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000390725 — 1 exons

Exon	Start	End
ENSE00001508402	147259652	147259726

Expression profiles

Bgee: expression breadth broad, 30 present calls, max score 74.38.

Top tissues by expression

30 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
endometrium	UBERON:0001295	74.38	gold quality
muscle layer of sigmoid colon	UBERON:0035805	74.07	gold quality
adult mammalian kidney	UBERON:0000082	73.36	gold quality
blood	UBERON:0000178	71.12	gold quality
prefrontal cortex	UBERON:0000451	70.18	gold quality
ascending aorta	UBERON:0001496	69.24	gold quality
right frontal lobe	UBERON:0002810	68.57	gold quality
right lobe of liver	UBERON:0001114	67.31	gold quality
esophagus mucosa	UBERON:0002469	67.30	gold quality
metanephros cortex	UBERON:0010533	67.00	gold quality
body of stomach	UBERON:0001161	66.34	gold quality
myometrium	UBERON:0001296	66.33	gold quality
colon	UBERON:0001155	66.08	gold quality
subcutaneous adipose tissue	UBERON:0002190	65.99	gold quality
intestine	UBERON:0000160	65.43	gold quality
transverse colon	UBERON:0001157	65.34	gold quality
multicellular organism	UBERON:0000468	64.94	gold quality
putamen	UBERON:0001874	64.76	gold quality
skin of abdomen	UBERON:0001416	64.35	gold quality
right lobe of thyroid gland	UBERON:0001119	63.44	gold quality
skin of leg	UBERON:0001511	62.63	gold quality
small intestine Peyer’s patch	UBERON:0003454	62.53	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	61.14	gold quality
spleen	UBERON:0002106	60.66	gold quality
urinary bladder	UBERON:0001255	60.35	gold quality
substantia nigra	UBERON:0002038	59.37	gold quality
tibial nerve	UBERON:0001323	58.32	gold quality
left ovary	UBERON:0002119	57.85	gold quality
corpus callosum	UBERON:0002336	55.10	gold quality
left testis	UBERON:0004533	44.44	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.34

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 24)

• miR-508-3p and miR-509-3p played an important role as tumor suppressor genes during tumor formation and that they may serve as novel diagnostic markers for RCC. (PMID:22369946)
• miR-509-5p plays an important role in renal cell carcinoma by inhibiting cell proliferation and migration and by promoting cell apoptosis. (PMID:23619562)
• inhibits cell proliferation, colony formation, and migration of cancer cells (PMID:24802056)
• HBXIP facilitates the proliferation of hepatoma cells by up-regulating SCG3 via E2F1 and miR-509-3p modulation. (PMID:24882622)
• Enforced miR-509 expression in NALM6 cells reduced RAB5C mRNA and protein levels, and RAB5C was demonstrated to be a direct target of miR-509. (PMID:25368993)
• the results of the present study demonstrated that the miR-509-3p RCC suppressor was a significant regulator of the MAP3K8 oncogene, suggesting that it may have a potential therapeutic role in the treatment of renal cell carcinoma (PMID:25815776)
• we identified microRNA-509-3p as a clinically significant microRNA in epithelial ovarian cancer (PMID:27036018)
• miR-509-3-5p is a strong suppressor of cancer via targeting PLK1. (PMID:27498003)
• Results revealed that miR-509-3-5P, an important antionco-miRNA associated with lymphatic metastasis, were decreased in gastric cancer (GC) tissues and cell lines. Ectopic expression of miR-509-3-5P in GC cell lines inhibited the colony, motility and invasion abilities via negatively targeting PODXL. (PMID:28432273)
• The co-transfection of the pLuc-CFTR-3 UTR vector with different combinations of PNAs, miR-509-3p, and controls in A549 cells demonstrated the ability of the longer PNA to rescue the luciferase activity by up to 70% of the control, thus supporting the use of suitable PNAs to counteract the reduction in the CFTR expression (PMID:28698463)
• MiR-509-5p exerted tumor-suppressive effects on breast cancer progression and metastasis via targeting SOD2 in vitro (PMID:28925482)
• Clinical diagnostic value of circulating serum miR-509-3p in pulmonary arterial hypertension with congenital heart disease. (PMID:29890280)
• Functional studies demonstrated that miR-509-3p inhibitor decreased cell response to cisplatin (CDDP) and promoted cell survival in SKOV3 ovarian cancer cells. (PMID:30408550)
• MicroRNA-509-3p inhibits cellular migration, invasion, and proliferation, and sensitizes osteosarcoma to cisplatin. (PMID:31836741)
• MiR-509-3 augments the synthetic lethality of PARPi by regulating HR repair in PDX model of HGSOC. (PMID:32005272)
• MiR-509-3-5p-NONHSAT112228.2 Axis Regulates p21 and Suppresses Proliferation and Migration of Lung Cancer Cells. (PMID:32141418)
• Knockdown of LINC00467 contributed to Axitinib sensitivity in hepatocellular carcinoma through miR-509-3p/PDGFRA axis. (PMID:32221502)
• Long noncoding RNA CBR3 antisense RNA 1 promotes the aggressive phenotypes of nonsmallcell lung cancer by sponging microRNA5093p and competitively upregulating HDAC9 expression. (PMID:32945466)
• Expression of the chrXq27.3 miRNA cluster in recurrent ovarian clear cell carcinoma and its impact on cisplatin resistance. (PMID:33420363)
• miR-509-3p Suppresses Migration, Invasion, and Epithelial- Mesenchymal Transition in Melanoma Cells by Targeting Collagen Triple Helix Repeat Containing 1. (PMID:33593721)
• MiR-509-3p Induces Apoptosis and Affects the Chemosensitivity of Cervical Cancer Cells by Targeting the RAC1/PAK1/LIMK1/Cofilin Pathway. (PMID:33790078)
• MicroRNA miR-509-3p inhibit metastasis and epithelial-mesenchymal transition in hepatocellular carcinoma. (PMID:34115554)
• MiR-509-3p is oncogenic, targets the tumor suppressor PHLPP2, and functions as a novel tumor adjacent normal tissue based prognostic biomarker in colorectal cancer. (PMID:35361144)
• miR-509-5p promotes colorectal cancer cell ferroptosis by targeting SLC7A11. (PMID:37229918)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Mir509	ENSMUSG00000106233

Paralogs (9): MIR506 (ENSG00000207731), MIR514A2 (ENSG00000207866), MIR514A3 (ENSG00000207867), MIR514A1 (ENSG00000207868), MIR513B (ENSG00000207871), MIR507 (ENSG00000207969), MIR513A2 (ENSG00000207984), MIR509-1 (ENSG00000208000), MIR514B (ENSG00000252583)

Protein

Non-coding RNA — no protein product; not a drug target.

Function

No curated pathway, Gene-Ontology, or interaction data.

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

No drug or pharmacology data — not an established drug target.