LINC00839

Summary

LINC00839 (long intergenic non-protein coding RNA 839, HGNC:28269) is a long non-coding RNA gene on chromosome 10q11.21.

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:28269
Approved symbol	LINC00839
Name	long intergenic non-protein coding RNA 839
Location	10q11.21
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000185904
Ensembl biotype	lncRNA
Entrez	84856
RNAcentral	URS000075BFEF — lncRNA, 2322 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 16 lncRNA

ENST00000424751, ENST00000429940, ENST00000653292, ENST00000659650, ENST00000662209, ENST00000667964, ENST00000668072, ENST00000670637, ENST00000670679, ENST00000797869, ENST00000797870, ENST00000797871, ENST00000797872, ENST00000797873, ENST00000797874, ENST00000797875

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000424751 — 5 exons

Exon	Start	End
ENSE00001539564	42492080	42492342
ENSE00001707345	42475628	42475964
ENSE00003232534	42486979	42487126
ENSE00003254970	42477261	42477442
ENSE00004184904	42494015	42495337

Expression profiles

Bgee: expression breadth ubiquitous, 164 present calls, max score 78.08.

FANTOM5 (CAGE): breadth broad, TPM avg 3.2062 / max 107.8972, expressed in 823 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
104731	1.6328	488
104732	1.1118	539
104733	0.2697	160
104734	0.1918	97

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
caudate nucleus	UBERON:0001873	78.08	gold quality
stromal cell of endometrium	CL:0002255	78.05	gold quality
adult mammalian kidney	UBERON:0000082	77.71	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.60	silver quality
nucleus accumbens	UBERON:0001882	75.91	gold quality
middle temporal gyrus	UBERON:0002771	75.44	gold quality
putamen	UBERON:0001874	74.61	gold quality
spleen	UBERON:0002106	74.56	gold quality
Brodmann (1909) area 9	UBERON:0013540	74.52	gold quality
prefrontal cortex	UBERON:0000451	74.46	gold quality
anterior cingulate cortex	UBERON:0009835	74.35	gold quality
right frontal lobe	UBERON:0002810	74.10	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	73.88	gold quality
amygdala	UBERON:0001876	73.39	gold quality
kidney epithelium	UBERON:0004819	73.31	gold quality
hypothalamus	UBERON:0001898	72.87	gold quality
kidney	UBERON:0002113	72.76	gold quality
neocortex	UBERON:0001950	71.92	gold quality
frontal cortex	UBERON:0001870	71.85	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	71.30	gold quality
cerebral cortex	UBERON:0000956	70.67	gold quality
islet of Langerhans	UBERON:0000006	70.30	gold quality
colonic epithelium	UBERON:0000397	70.19	silver quality
Brodmann (1909) area 23	UBERON:0013554	70.17	gold quality
cortex of kidney	UBERON:0001225	70.03	gold quality
forebrain	UBERON:0001890	69.62	gold quality
seminal vesicle	UBERON:0000998	69.40	gold quality
smooth muscle tissue	UBERON:0001135	69.36	gold quality
upper lobe of left lung	UBERON:0008952	68.93	gold quality
temporal lobe	UBERON:0001871	68.65	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.67

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 8)

• LINC00839/miR-519d-3p/JMJD6 axis modulated cell viability, apoptosis, migration and invasiveness of lung cancer cells. (PMID:34734406)
• [Effects of LINC00839 targeting miR-3666 on proliferation, migration and invasion of hepatocellular carcinoma cells]. (PMID:34794216)
• LINC00839 Promotes Neuroblastoma Progression by Sponging miR-454-3p to Up-Regulate NEUROD1. (PMID:35606572)
• LINC00839 promotes colorectal cancer progression by recruiting RUVBL1/Tip60 complexes to activate NRF1. (PMID:35876654)
• LINC00839 promotes malignancy of liver cancer via binding FMNL2 under hypoxia. (PMID:36335129)
• m6A-enriched lncRNA LINC00839 promotes tumor progression by enhancing TAF15-mediated transcription of amine oxidase AOC1 in nasopharyngeal carcinoma. (PMID:37257820)
• METTL3-mediated m6A modification of LINC00839 maintains glioma stem cells and radiation resistance by activating Wnt/beta-catenin signaling. (PMID:37438359)
• EGR1/LINC00839/SOX5 axis modulates migration, invasion and Gemcitabine resistance of bladder cancer cells. (PMID:37862152)

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.