LINC00239

Summary

LINC00239 (long intergenic non-protein coding RNA 239, HGNC:20119) is a long non-coding RNA gene on chromosome 14q32.31.

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:20119
Approved symbol	LINC00239
Name	long intergenic non-protein coding RNA 239
Location	14q32.31
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000258512
Ensembl biotype	lncRNA
Entrez	145200
RNAcentral	URS000075D38E — lncRNA, 662 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 lncRNA

ENST00000556973, ENST00000755272, ENST00000755273

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000556973 — 4 exons

Exon	Start	End
ENSE00002430271	101730437	101730487
ENSE00002534896	101731788	101731976
ENSE00003986255	101731357	101731468
ENSE00003986256	101732236	101732534

Expression profiles

Bgee: expression breadth ubiquitous, 115 present calls, max score 74.13.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0657 / max 17.7375, expressed in 29 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
141589	0.0657	29

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lymph node	UBERON:0000029	74.13	gold quality
tonsil	UBERON:0002372	71.49	gold quality
vermiform appendix	UBERON:0001154	71.22	gold quality
granulocyte	CL:0000094	71.17	gold quality
blood	UBERON:0000178	68.55	gold quality
body of pancreas	UBERON:0001150	67.25	gold quality
pancreas	UBERON:0001264	67.01	gold quality
islet of Langerhans	UBERON:0000006	66.64	gold quality
bone marrow cell	CL:0002092	66.51	silver quality
mucosa of transverse colon	UBERON:0004991	66.30	gold quality
spleen	UBERON:0002106	64.34	gold quality
pituitary gland	UBERON:0000007	64.23	gold quality
rectum	UBERON:0001052	63.84	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	63.70	gold quality
nucleus accumbens	UBERON:0001882	63.39	gold quality
small intestine Peyer’s patch	UBERON:0003454	62.77	gold quality
small intestine	UBERON:0002108	62.67	gold quality
gall bladder	UBERON:0002110	62.46	gold quality
adenohypophysis	UBERON:0002196	62.28	gold quality
bone marrow	UBERON:0002371	62.11	gold quality
leukocyte	CL:0000738	61.46	gold quality
putamen	UBERON:0001874	60.57	gold quality
right lung	UBERON:0002167	60.10	gold quality
caudate nucleus	UBERON:0001873	59.51	gold quality
prefrontal cortex	UBERON:0000451	58.25	gold quality
saliva-secreting gland	UBERON:0001044	58.12	gold quality
minor salivary gland	UBERON:0001830	57.81	gold quality
muscle tissue	UBERON:0002385	57.81	gold quality
duodenum	UBERON:0002114	57.77	gold quality
intestine	UBERON:0000160	57.36	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.47

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• LINC00239 Interacts with C-Myc Promoter-Binding Protein-1 (MBP-1) to Promote Expression of C-Myc in Esophageal Squamous Cell Carcinoma. (PMID:34016746)
• Long noncoding RNA LINC00239 inhibits ferroptosis in colorectal cancer by binding to Keap1 to stabilize Nrf2. (PMID:36038548)
• Linc00239 Promotes Colorectal Cancer Development via MicroRNA-182-5p/Metadherin Axis. (PMID:37695492)

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.