LINC01090

Summary

LINC01090 (long intergenic non-protein coding RNA 1090, HGNC:49201) is a long non-coding RNA gene on chromosome 2q32.1.

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:49201
Approved symbol	LINC01090
Name	long intergenic non-protein coding RNA 1090
Location	2q32.1
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000231689
Ensembl biotype	lncRNA
Entrez	104355152
RNAcentral	URS00007E3DBF — lncRNA, 496 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 13 lncRNA

ENST00000415357, ENST00000434418, ENST00000632331, ENST00000685790, ENST00000757430, ENST00000757431, ENST00000757432, ENST00000757433, ENST00000757434, ENST00000757435, ENST00000757436, ENST00000803541, ENST00000847180

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000415357 — 2 exons

Exon	Start	End
ENSE00001511586	188227820	188228532
ENSE00001617823	188287467	188287634

Expression profiles

Bgee: expression breadth ubiquitous, 118 present calls, max score 80.17.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0363 / max 7.1148, expressed in 19 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
32826	0.0363	19

Top tissues by expression

118 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	80.17	silver quality
sural nerve	UBERON:0015488	70.43	gold quality
cortical plate	UBERON:0005343	68.68	gold quality
ventricular zone	UBERON:0003053	65.92	gold quality
anterior cingulate cortex	UBERON:0009835	64.68	gold quality
placenta	UBERON:0001987	64.39	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	64.14	gold quality
skeletal muscle tissue	UBERON:0001134	64.12	silver quality
prefrontal cortex	UBERON:0000451	64.01	gold quality
ganglionic eminence	UBERON:0004023	63.61	gold quality
superior frontal gyrus	UBERON:0002661	62.62	gold quality
frontal cortex	UBERON:0001870	62.16	gold quality
cerebral cortex	UBERON:0000956	61.05	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	60.56	gold quality
right frontal lobe	UBERON:0002810	60.52	gold quality
Brodmann (1909) area 9	UBERON:0013540	58.90	gold quality
lower esophagus mucosa	UBERON:0035834	57.70	gold quality
monocyte	CL:0000576	57.69	gold quality
primary visual cortex	UBERON:0002436	54.68	gold quality
calcaneal tendon	UBERON:0003701	54.45	gold quality
brain	UBERON:0000955	54.25	gold quality
temporal lobe	UBERON:0001871	53.52	gold quality
amygdala	UBERON:0001876	53.41	gold quality
islet of Langerhans	UBERON:0000006	53.32	gold quality
fundus of stomach	UBERON:0001160	53.16	gold quality
blood	UBERON:0000178	52.43	gold quality
duodenum	UBERON:0002114	52.30	gold quality
descending thoracic aorta	UBERON:0002345	51.82	gold quality
right uterine tube	UBERON:0001302	51.66	gold quality
vermiform appendix	UBERON:0001154	51.62	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.04

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• AC068718.1 is a designator for the locus represented in HGNC as LINC01090 (PMID:24080187)
• findings implicate a novel RNA gene, lincRNA AC068718.1, as risk factor for post-traumatic stress disorder in women [lincRNA AC068718.1] (PMID:24080187)

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.