LINC00540

Summary

LINC00540 (long intergenic non-protein coding RNA 540, HGNC:43673) 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:43673
Approved symbol	LINC00540
Name	long intergenic non-protein coding RNA 540
Location	13q12.11
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000276476
Ensembl biotype	lncRNA
Entrez	100506622
RNAcentral	URS000075ACCF — lncRNA, 2156 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 22 lncRNA

ENST00000611481, ENST00000616974, ENST00000631321, ENST00000655363, ENST00000656522, ENST00000657205, ENST00000658741, ENST00000659301, ENST00000690279, ENST00000721755, ENST00000721756, ENST00000721757, ENST00000721758, ENST00000721759, ENST00000721760, ENST00000721761, ENST00000721762, ENST00000721763, ENST00000721764, ENST00000721765, ENST00000721766, ENST00000721767

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000611481 — 2 exons

Exon	Start	End
ENSE00003725622	22107470	22107634
ENSE00003743629	22274523	22274945

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 84.84.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5953 / max 91.3627, expressed in 214 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
134351	0.5953	214

Top tissues by expression

226 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	84.84	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.54	gold quality
buccal mucosa cell	CL:0002336	77.89	gold quality
bone marrow cell	CL:0002092	65.95	silver quality
granulocyte	CL:0000094	63.52	gold quality
left adrenal gland	UBERON:0001234	62.05	gold quality
placenta	UBERON:0001987	62.02	gold quality
left adrenal gland cortex	UBERON:0035825	61.57	gold quality
right adrenal gland cortex	UBERON:0035827	61.53	gold quality
adrenal gland	UBERON:0002369	60.57	gold quality
right adrenal gland	UBERON:0001233	60.42	gold quality
adrenal cortex	UBERON:0001235	60.07	gold quality
heart left ventricle	UBERON:0002084	60.01	gold quality
apex of heart	UBERON:0002098	59.82	gold quality
cardiac ventricle	UBERON:0002082	59.34	gold quality
adrenal tissue	UBERON:0018303	57.95	gold quality
leukocyte	CL:0000738	57.17	gold quality
endometrium	UBERON:0001295	56.87	gold quality
metanephros cortex	UBERON:0010533	56.14	gold quality
heart	UBERON:0000948	54.80	gold quality
monocyte	CL:0000576	54.41	gold quality
lymph node	UBERON:0000029	54.33	gold quality
smooth muscle tissue	UBERON:0001135	54.14	gold quality
islet of Langerhans	UBERON:0000006	53.73	gold quality
prefrontal cortex	UBERON:0000451	53.40	gold quality
hindlimb stylopod muscle	UBERON:0004252	53.39	silver quality
uterus	UBERON:0000995	53.04	gold quality
gall bladder	UBERON:0002110	52.90	gold quality
vermiform appendix	UBERON:0001154	52.61	gold quality
calcaneal tendon	UBERON:0003701	52.56	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.91

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Associations between LINC00540 rs9316871 and ERG rs2836411 and abdominal aortic aneurysm (AAA) risk were replicated in the meta-analysis of the two independent cohorts from, providing further support for the importance of these loci in the etiology of AAA.[meta-analysis] (PMID:31680049)

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.