LINC00534

Summary

LINC00534 (long intergenic non-protein coding RNA 534, HGNC:43643) is a long non-coding RNA gene on chromosome 8q21.3.

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:43643
Approved symbol	LINC00534
Name	long intergenic non-protein coding RNA 534
Location	8q21.3
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000253394
Ensembl biotype	lncRNA
Entrez	100874052
RNAcentral	URS000075ABFF — lncRNA, 869 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 27 lncRNA

ENST00000517400, ENST00000523283, ENST00000523406, ENST00000524361, ENST00000653734, ENST00000654785, ENST00000654946, ENST00000655123, ENST00000655219, ENST00000655523, ENST00000658299, ENST00000658342, ENST00000659030, ENST00000661519, ENST00000662145, ENST00000662692, ENST00000663098, ENST00000663329, ENST00000663619, ENST00000665280, ENST00000666641, ENST00000667296, ENST00000667565, ENST00000668720, ENST00000668745, ENST00000670903, ENST00000671657

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000517400 — 4 exons

Exon	Start	End
ENSE00002122579	90387567	90388593
ENSE00002123572	90246180	90246270
ENSE00002127002	90221647	90221746
ENSE00002131398	90221479	90221510

Expression profiles

Bgee: expression breadth ubiquitous, 130 present calls, max score 86.01.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.4914 / max 551.2229, expressed in 79 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
89696	0.6357	69
89694	0.6265	61
89698	0.1256	44
89697	0.0750	33
89695	0.0287	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.01	gold quality
monocyte	CL:0000576	81.38	gold quality
leukocyte	CL:0000738	79.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.08	gold quality
corpus callosum	UBERON:0002336	76.06	gold quality
colonic epithelium	UBERON:0000397	65.56	silver quality
adrenal tissue	UBERON:0018303	65.48	gold quality
calcaneal tendon	UBERON:0003701	64.85	gold quality
testis	UBERON:0000473	64.06	gold quality
blood	UBERON:0000178	63.29	gold quality
nucleus accumbens	UBERON:0001882	62.71	gold quality
cortical plate	UBERON:0005343	62.44	gold quality
ventricular zone	UBERON:0003053	62.40	gold quality
right testis	UBERON:0004534	62.19	gold quality
left testis	UBERON:0004533	62.08	gold quality
sural nerve	UBERON:0015488	61.34	gold quality
granulocyte	CL:0000094	60.39	gold quality
stromal cell of endometrium	CL:0002255	60.17	gold quality
ganglionic eminence	UBERON:0004023	59.89	gold quality
superior frontal gyrus	UBERON:0002661	59.45	gold quality
liver	UBERON:0002107	59.27	gold quality
hindlimb stylopod muscle	UBERON:0004252	58.68	gold quality
right lobe of liver	UBERON:0001114	58.48	gold quality
skeletal muscle tissue	UBERON:0001134	56.88	gold quality
prefrontal cortex	UBERON:0000451	56.87	gold quality
primary visual cortex	UBERON:0002436	56.65	gold quality
endometrium	UBERON:0001295	56.39	gold quality
bone marrow	UBERON:0002371	55.33	gold quality
apex of heart	UBERON:0002098	55.30	gold quality
frontal cortex	UBERON:0001870	55.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.25

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• LncRNA LINC00534 regulates cell proliferation and migration via the miR-494-3p/PTEN axis in HTR-8/SVneo cells. (PMID:36478207)

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.