LINC01239

Summary

LINC01239 (long intergenic non-protein coding RNA 1239, HGNC:49796) is a long non-coding RNA gene on chromosome 9p21.3.

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:49796
Approved symbol	LINC01239
Name	long intergenic non-protein coding RNA 1239
Location	9p21.3
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000234840
Ensembl biotype	lncRNA
Entrez	441389
RNAcentral	URS00000E9163 — lncRNA, 2347 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 lncRNA, 1 retained_intron

ENST00000433645, ENST00000436786, ENST00000669551, ENST00000764418

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000433645 — 2 exons

Exon	Start	End
ENSE00001647776	22682470	22682713
ENSE00001702469	22687547	22687627

Expression profiles

Bgee: expression breadth ubiquitous, 119 present calls, max score 79.79.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2130 / max 35.2686, expressed in 50 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
96339	0.1321	41
96337	0.0475	17
96338	0.0335	19

Top tissues by expression

119 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	79.79	gold quality
subcutaneous adipose tissue	UBERON:0002190	72.87	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	70.89	gold quality
sural nerve	UBERON:0015488	70.25	gold quality
liver	UBERON:0002107	68.87	gold quality
right lobe of liver	UBERON:0001114	66.33	gold quality
mucosa of stomach	UBERON:0001199	65.96	gold quality
adipose tissue	UBERON:0001013	65.71	gold quality
thoracic mammary gland	UBERON:0005200	65.15	gold quality
monocyte	CL:0000576	62.32	gold quality
gastrocnemius	UBERON:0001388	62.31	gold quality
muscle of leg	UBERON:0001383	62.24	gold quality
esophagus mucosa	UBERON:0002469	62.21	gold quality
minor salivary gland	UBERON:0001830	61.85	gold quality
saliva-secreting gland	UBERON:0001044	61.84	gold quality
esophagus	UBERON:0001043	61.18	gold quality
hindlimb stylopod muscle	UBERON:0004252	61.11	gold quality
skeletal muscle tissue	UBERON:0001134	60.23	gold quality
lower esophagus muscularis layer	UBERON:0035833	60.12	gold quality
lower esophagus	UBERON:0013473	60.04	gold quality
cortical plate	UBERON:0005343	60.00	silver quality
urinary bladder	UBERON:0001255	59.90	gold quality
calcaneal tendon	UBERON:0003701	59.84	gold quality
tonsil	UBERON:0002372	59.64	gold quality
ganglionic eminence	UBERON:0004023	58.64	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	58.30	gold quality
ventricular zone	UBERON:0003053	58.18	silver quality
lower esophagus mucosa	UBERON:0035834	57.39	gold quality
omental fat pad	UBERON:0010414	56.90	gold quality
lung	UBERON:0002048	56.81	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.32

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.