LINC00472

Summary

LINC00472 (long intergenic non-protein coding RNA 472, HGNC:21380) is a long non-coding RNA gene on chromosome 6q13.

Predicted to be involved in miRNA-mediated post-transcriptional gene silencing. Predicted to be part of RISC complex.

Source: NCBI Gene 79940 — RefSeq curated summary.

At a glance

• Gene type: non-coding (lncRNA) — 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:21380
Approved symbol	LINC00472
Name	long intergenic non-protein coding RNA 472
Location	6q13
Locus type	RNA, long non-coding
Status	Approved
Aliases	PEXF, P53RRA, FLJ13189, dJ288M22.3
Ensembl gene	ENSG00000233237
Ensembl biotype	lncRNA
OMIM	620059
Entrez	79940
RNAcentral	URS000075F08B — lncRNA, 9566 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 65 — 65 lncRNA

ENST00000412751, ENST00000413945, ENST00000421704, ENST00000423255, ENST00000426635, ENST00000432050, ENST00000434683, ENST00000436803, ENST00000441570, ENST00000450998, ENST00000585882, ENST00000585945, ENST00000586030, ENST00000586232, ENST00000586974, ENST00000587015, ENST00000587036, ENST00000587253, ENST00000587397, ENST00000588612, ENST00000589255, ENST00000590213, ENST00000590780, ENST00000591156, ENST00000602418, ENST00000602823, ENST00000602878, ENST00000612512, ENST00000614602, ENST00000615921, ENST00000618488, ENST00000625013, ENST00000650942, ENST00000651660, ENST00000651778, ENST00000652370, ENST00000652523, ENST00000652655, ENST00000652746, ENST00000710850, ENST00000710851, ENST00000725030, ENST00000725031, ENST00000725032, ENST00000725033, ENST00000725034, ENST00000725035, ENST00000725036, ENST00000725037, ENST00000725038, ENST00000725039, ENST00000725040, ENST00000725041, ENST00000725042, ENST00000725043, ENST00000725044, ENST00000725045, ENST00000725046, ENST00000725047, ENST00000725048, ENST00000725049, ENST00000725050, ENST00000725051, ENST00000725052, ENST00000725053

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000412751 — 4 exons

Exon	Start	End
ENSE00001611562	71277219	71277314
ENSE00001624199	71310550	71310576
ENSE00001736057	71251358	71251621
ENSE00003558001	71310296	71310373

Expression profiles

Bgee: expression breadth ubiquitous, 197 present calls, max score 92.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.8517 / max 140.0569, expressed in 1156 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
74335	3.7520	1084
74333	0.4977	241
74334	0.2357	125
74332	0.1908	96
74331	0.1754	61

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
metanephros cortex	UBERON:0010533	92.49	gold quality
sural nerve	UBERON:0015488	89.31	gold quality
right lung	UBERON:0002167	87.84	gold quality
renal medulla	UBERON:0000362	86.60	gold quality
colonic epithelium	UBERON:0000397	83.74	gold quality
right lobe of thyroid gland	UBERON:0001119	83.41	gold quality
left lobe of thyroid gland	UBERON:0001120	83.15	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.94	gold quality
cortex of kidney	UBERON:0001225	82.80	gold quality
thyroid gland	UBERON:0002046	82.32	gold quality
endothelial cell	CL:0000115	82.20	silver quality
kidney	UBERON:0002113	82.20	gold quality
adult mammalian kidney	UBERON:0000082	82.17	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.31	gold quality
upper lobe of left lung	UBERON:0008952	81.09	gold quality
body of pancreas	UBERON:0001150	80.71	gold quality
upper lobe of lung	UBERON:0008948	80.36	gold quality
calcaneal tendon	UBERON:0003701	78.88	gold quality
metanephros	UBERON:0000081	78.84	gold quality
hindlimb stylopod muscle	UBERON:0004252	78.60	gold quality
lower esophagus muscularis layer	UBERON:0035833	77.73	gold quality
popliteal artery	UBERON:0002250	77.68	gold quality
tibial artery	UBERON:0007610	77.64	gold quality
lower esophagus	UBERON:0013473	77.63	gold quality
apex of heart	UBERON:0002098	76.94	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	76.92	gold quality
aorta	UBERON:0000947	76.62	gold quality
minor salivary gland	UBERON:0001830	76.61	gold quality
left coronary artery	UBERON:0001626	76.36	gold quality
gastrocnemius	UBERON:0001388	76.24	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	43.06
E-ANND-3	yes	11.23

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 16)

• Patients with high LINC00472 had significantly reduced risk of relapse and death, and they also had more favorable subtypes and better responses to adjuvant chemo- or hormonal therapy. (PMID:25865225)
• LINC00472 is functionally a tumor suppressor.LINC00472 expression is regulated by promoter methylation and associated with disease-free survival in patients with grade 2 breast cancer. (PMID:26564482)
• These results may provide a clue to further research into the function and regulatory mechanism of LINC00472 in colorectal cancer. (PMID:29488624)
• Study demonstrated that the cytosolic lncRNA P53RRA is downregulated in cancers and functions as a tumor suppressor by inhibiting cancer progression. P53RRA bound G3BP1 and cytosolic P53RRA-G3BP1 interaction displaced p53 from a G3BP1 complex, resulting in greater p53 retention in the nucleus, which led to cell-cycle arrest, apoptosis, and ferroptosis. (PMID:29588351)
• This study identified EA15, MIR22, and LINC00472 may serve as the potential diagnostic markers of diabetic nephropathy. (PMID:30317603)
• LINC00472 suppressed proliferation, migration and invasion of hepatocellular carcinoma cells. MiR-93-5p was a direct target of LINC00472, and miR-93-5p directly targeted PDCD4. The miR-93-5p/PDCD4 pathway mediated the suppressing role of LINC00472 in hepatocellular carcinoma cells. As an important tumor suppressor, LINC00472 could be used as a bio-marker for HCC therapy. (PMID:30522853)
• The study demonstrates that ERa upregulates LINC00472 which suppresses the phosphorylation of NF-kappaB, and suggests that endocrine treatment may lower LINC00472 and increase NF-kappaB activities, leading to tumor progression and disease recurrence (PMID:30830488)
• Dysregulated expression of LINC00472 in atrial fibrillation patients could up-regulate the expression of miR-24, a competing endogenous RNA of LINC00472, resulting in the deregulation of JP2 and RyR2, which may contribute to the pathogenesis of AF. (PMID:31562981)
• LINC00472 promotes osteogenic differentiation and alleviates osteoporosis by sponging miR-300 to upregulate the expression of FGFR2. (PMID:32432728)
• Down-regulation of long noncoding RNA LINC00472 alleviates sepsis-induced acute hepatic injury by regulating miR-373-3p/TRIM8 axis. (PMID:33129786)
• LncRNA LINC00472 regulates cell stiffness and inhibits the migration and invasion of lung adenocarcinoma by binding to YBX1. (PMID:33144579)
• LINC00472 suppressed by ZEB1 regulates the miR-23a-3p/FOXO3/BID axis to inhibit the progression of pancreatic cancer. (PMID:34363438)
• Gene expression profiling after LINC00472 overexpression in an NSCLC cell line1. (PMID:34397405)
• Long non-coding RNA LINC00472 inhibits oral squamous cell carcinoma via miR-4311/GNG7 axis. (PMID:35240924)
• LINC00472 suppresses oral squamous cell carcinoma growth by targeting miR-455-3p/ELF3 axis. (PMID:35258410)
• LINC00472 suppresses non-small cell lung cancer progression via regulating miR-23a-3p/CCL22 axis. (PMID:38836681)

Cross-species orthologs

0 orthologs

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.