LINC00539

Summary

LINC00539 (long intergenic non-protein coding RNA 539, HGNC:43672) is a long non-coding RNA gene on chromosome 13q12.11.

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:43672
Approved symbol	LINC00539
Name	long intergenic non-protein coding RNA 539
Location	13q12.11
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000224429
Ensembl biotype	lncRNA
Entrez	100652865
RNAcentral	URS000075B2E9 — lncRNA, 911 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 36 — 36 lncRNA

ENST00000411525, ENST00000423575, ENST00000434601, ENST00000608957, ENST00000655569, ENST00000657403, ENST00000659153, ENST00000659380, ENST00000661173, ENST00000661286, ENST00000664392, ENST00000664989, ENST00000667082, ENST00000670912, ENST00000692188, ENST00000700722, ENST00000700723, ENST00000700724, ENST00000753374, ENST00000753375, ENST00000753376, ENST00000753377, ENST00000753378, ENST00000753379, ENST00000753380, ENST00000753381, ENST00000753382, ENST00000753383, ENST00000753384, ENST00000753385, ENST00000753386, ENST00000753387, ENST00000753388, ENST00000753389, ENST00000753390, ENST00000753391

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000411525 — 5 exons

Exon	Start	End
ENSE00001483246	21347312	21347539
ENSE00001611665	21325625	21325815
ENSE00001728643	21330574	21330658
ENSE00001761531	21344666	21344786
ENSE00001765987	21348683	21348721

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 81.81.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1055 / max 13.9562, expressed in 32 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
136385	0.1055	32

Top tissues by expression

137 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	81.81	gold quality
right uterine tube	UBERON:0001302	78.47	gold quality
bone marrow	UBERON:0002371	76.75	gold quality
granulocyte	CL:0000094	76.28	gold quality
bone marrow cell	CL:0002092	75.80	gold quality
cortical plate	UBERON:0005343	75.70	gold quality
blood	UBERON:0000178	74.67	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	74.40	gold quality
lymph node	UBERON:0000029	74.37	gold quality
spinal cord	UBERON:0002240	74.30	gold quality
testis	UBERON:0000473	73.33	gold quality
left testis	UBERON:0004533	73.20	gold quality
right testis	UBERON:0004534	73.06	gold quality
corpus callosum	UBERON:0002336	72.81	gold quality
pituitary gland	UBERON:0000007	71.82	gold quality
colonic epithelium	UBERON:0000397	71.54	gold quality
spleen	UBERON:0002106	71.53	gold quality
endometrium	UBERON:0001295	71.49	gold quality
fallopian tube	UBERON:0003889	71.40	gold quality
substantia nigra	UBERON:0002038	71.26	gold quality
smooth muscle tissue	UBERON:0001135	71.22	gold quality
thyroid gland	UBERON:0002046	71.04	gold quality
right lobe of thyroid gland	UBERON:0001119	71.01	gold quality
right coronary artery	UBERON:0001625	70.86	gold quality
adenohypophysis	UBERON:0002196	70.82	gold quality
left lobe of thyroid gland	UBERON:0001120	70.80	gold quality
placenta	UBERON:0001987	70.63	gold quality
leukocyte	CL:0000738	70.53	gold quality
monocyte	CL:0000576	70.42	gold quality
body of uterus	UBERON:0009853	70.23	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.39

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.