LINC01539

Summary

LINC01539 (long intergenic non-protein coding RNA 1539, HGNC:51307) is a long non-coding RNA gene on chromosome 18q21.2.

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:51307
Approved symbol	LINC01539
Name	long intergenic non-protein coding RNA 1539
Location	18q21.2
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000267712
Ensembl biotype	lncRNA
Entrez	100505474
RNAcentral	URS0000759985 — lncRNA, 2093 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 72 — 72 lncRNA

ENST00000382897, ENST00000587904, ENST00000589293, ENST00000589447, ENST00000589617, ENST00000589754, ENST00000590484, ENST00000591974, ENST00000593282, ENST00000650203, ENST00000653524, ENST00000653652, ENST00000654820, ENST00000655121, ENST00000655648, ENST00000656570, ENST00000656913, ENST00000657412, ENST00000660365, ENST00000660685, ENST00000661430, ENST00000662269, ENST00000662324, ENST00000662735, ENST00000663100, ENST00000664250, ENST00000664576, ENST00000664842, ENST00000665019, ENST00000665833, ENST00000666910, ENST00000668386, ENST00000668690, ENST00000669575, ENST00000670316, ENST00000670613, ENST00000671257, ENST00000671420, ENST00000671483, ENST00000671593, ENST00000714785, ENST00000715823, ENST00000765110, ENST00000765111, ENST00000765112, ENST00000765113, ENST00000765114, ENST00000765115, ENST00000765116, ENST00000765117, ENST00000765118, ENST00000765119, ENST00000765120, ENST00000765121, ENST00000765122, ENST00000765123, ENST00000765124, ENST00000765125, ENST00000765126, ENST00000765127, ENST00000765128, ENST00000765129, ENST00000765130, ENST00000765131, ENST00000765132, ENST00000765133, ENST00000765134, ENST00000765135, ENST00000765136, ENST00000765137, ENST00000765138, ENST00000765139

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000382897 — 9 exons

Exon	Start	End
ENSE00001493733	56027797	56028940
ENSE00001493734	56055905	56056054
ENSE00001493737	56060104	56060204
ENSE00001542648	56003613	56003904
ENSE00001542649	56025341	56025395
ENSE00001542654	56181349	56181474
ENSE00001542655	56188278	56188350
ENSE00001542656	56190764	56191262
ENSE00001752551	56056542	56056659

Expression profiles

Bgee: expression breadth ubiquitous, 114 present calls, max score 96.06.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0058 / max 4.5108, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
172086	0.0058	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	96.06	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.82	gold quality
left testis	UBERON:0004533	87.62	gold quality
right testis	UBERON:0004534	87.07	gold quality
testis	UBERON:0000473	85.17	gold quality
right lobe of thyroid gland	UBERON:0001119	76.30	gold quality
left lobe of thyroid gland	UBERON:0001120	75.95	gold quality
thyroid gland	UBERON:0002046	75.34	gold quality
tibialis anterior	UBERON:0001385	66.87	silver quality
ileal mucosa	UBERON:0000331	65.61	silver quality
upper arm skin	UBERON:0004263	65.57	gold quality
left uterine tube	UBERON:0001303	64.66	gold quality
cardiac muscle of right atrium	UBERON:0003379	64.28	gold quality
left ventricle myocardium	UBERON:0006566	64.02	gold quality
adult organism	UBERON:0007023	62.40	gold quality
pancreatic ductal cell	CL:0002079	62.08	silver quality
lower esophagus mucosa	UBERON:0035834	61.87	gold quality
lymph node	UBERON:0000029	60.12	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	58.01	gold quality
endothelial cell	CL:0000115	57.43	gold quality
left ovary	UBERON:0002119	57.15	gold quality
calcaneal tendon	UBERON:0003701	56.44	gold quality
tendon of biceps brachii	UBERON:0008188	56.30	gold quality
myocardium	UBERON:0002349	55.53	gold quality
monocyte	CL:0000576	55.36	gold quality
vermiform appendix	UBERON:0001154	55.21	gold quality
epithelial cell of pancreas	CL:0000083	54.90	gold quality
tonsil	UBERON:0002372	53.95	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
gall bladder	UBERON:0002110	53.45	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.90

Regulation

Is transcription factor: no

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.