LINC01546

Summary

LINC01546 (long intergenic non-protein coding RNA 1546, HGNC:27336) is a long non-coding RNA gene on chromosome Xp22.33.

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:27336
Approved symbol	LINC01546
Name	long intergenic non-protein coding RNA 1546
Location	Xp22.33
Locus type	RNA, long non-coding
Status	Approved
Aliases	VAL
Ensembl gene	ENSG00000228459
Ensembl biotype	lncRNA
OMIM	301143
Entrez	100129464
RNAcentral	URS000075B7AF — lncRNA, 687 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 lncRNA

ENST00000457435, ENST00000656741, ENST00000668004, ENST00000668035, ENST00000686467, ENST00000688525, ENST00000796717, ENST00000796718, ENST00000796719, ENST00000796720, ENST00000796721, ENST00000796722

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000457435 — 3 exons

Exon	Start	End
ENSE00001791231	3272297	3272372
ENSE00004182644	3271504	3271918
ENSE00004182645	3284155	3286138

Expression profiles

Bgee: expression breadth ubiquitous, 125 present calls, max score 75.97.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1443 / max 14.2436, expressed in 64 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
195406	0.0854	45
195407	0.0589	37

Top tissues by expression

129 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	75.97	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	67.60	gold quality
bone marrow	UBERON:0002371	66.65	silver quality
skeletal muscle tissue	UBERON:0001134	66.08	gold quality
amygdala	UBERON:0001876	65.78	gold quality
temporal lobe	UBERON:0001871	65.68	gold quality
stromal cell of endometrium	CL:0002255	65.67	gold quality
quadriceps femoris	UBERON:0001377	65.49	gold quality
prefrontal cortex	UBERON:0000451	65.37	gold quality
anterior cingulate cortex	UBERON:0009835	65.35	gold quality
spinal cord	UBERON:0002240	65.03	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	65.01	gold quality
Ammon’s horn	UBERON:0001954	64.83	gold quality
cerebellar vermis	UBERON:0004720	64.61	gold quality
hindlimb stylopod muscle	UBERON:0004252	64.59	gold quality
gastrocnemius	UBERON:0001388	63.99	gold quality
muscle of leg	UBERON:0001383	63.93	gold quality
superior frontal gyrus	UBERON:0002661	63.43	gold quality
nucleus accumbens	UBERON:0001882	63.32	gold quality
cerebral cortex	UBERON:0000956	63.03	gold quality
frontal cortex	UBERON:0001870	62.73	gold quality
substantia nigra	UBERON:0002038	62.53	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	61.71	gold quality
primary visual cortex	UBERON:0002436	61.42	gold quality
brain	UBERON:0000955	60.71	gold quality
putamen	UBERON:0001874	60.64	gold quality
thymus	UBERON:0002370	60.39	silver quality
ganglionic eminence	UBERON:0004023	60.39	gold quality
caudate nucleus	UBERON:0001873	59.91	gold quality
Brodmann (1909) area 9	UBERON:0013540	59.72	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.95

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• AKT-induced lncRNA VAL promotes EMT-independent metastasis through diminishing Trim16-dependent Vimentin degradation. (PMID:33046716)

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.