LINC01339

Summary

LINC01339 (long intergenic non-protein coding RNA 1339, HGNC:50549) is a long non-coding RNA gene on chromosome 5q14.3.

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:50549
Approved symbol	LINC01339
Name	long intergenic non-protein coding RNA 1339
Location	5q14.3
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000248555
Ensembl biotype	lncRNA
Entrez	101929495
RNAcentral	URS0000759F60 — lncRNA, 573 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 33 — 32 lncRNA, 1 retained_intron

ENST00000505712, ENST00000518436, ENST00000519336, ENST00000524094, ENST00000658685, ENST00000660853, ENST00000664570, ENST00000667644, ENST00000669667, ENST00000670522, ENST00000813478, ENST00000813479, ENST00000813480, ENST00000813481, ENST00000813482, ENST00000813483, ENST00000813484, ENST00000813485, ENST00000813486, ENST00000813487, ENST00000813488, ENST00000813489, ENST00000813490, ENST00000813491, ENST00000813492, ENST00000813493, ENST00000813494, ENST00000813495, ENST00000813496, ENST00000813497, ENST00000813498, ENST00000813499, ENST00000813500

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000505712 — 6 exons

Exon	Start	End
ENSE00002023317	90200467	90200528
ENSE00002029115	90260546	90260586
ENSE00002048729	90160529	90160589
ENSE00002076940	90261668	90261719
ENSE00004213577	90158339	90158519
ENSE00004213580	90289896	90290040

Expression profiles

Bgee: expression breadth broad, 69 present calls, max score 83.31.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0118 / max 14.4347, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
62517	0.0118	3

Top tissues by expression

180 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
upper arm skin	UBERON:0004263	83.31	gold quality
left ventricle myocardium	UBERON:0006566	83.05	gold quality
cardiac muscle of right atrium	UBERON:0003379	82.97	gold quality
islet of Langerhans	UBERON:0000006	82.67	gold quality
right testis	UBERON:0004534	78.46	gold quality
left testis	UBERON:0004533	76.87	gold quality
epithelial cell of pancreas	CL:0000083	76.01	gold quality
myocardium	UBERON:0002349	75.78	gold quality
buccal mucosa cell	CL:0002336	75.38	silver quality
kidney epithelium	UBERON:0004819	74.92	gold quality
pancreatic ductal cell	CL:0002079	74.35	silver quality
testis	UBERON:0000473	74.21	gold quality
nasal cavity epithelium	UBERON:0005384	70.12	gold quality
sperm	CL:0000019	69.88	silver quality
ganglionic eminence	UBERON:0004023	67.83	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	67.81	gold quality
quadriceps femoris	UBERON:0001377	66.32	gold quality
deltoid	UBERON:0001476	66.22	gold quality
epithelium of nasopharynx	UBERON:0001951	66.15	gold quality
ileal mucosa	UBERON:0000331	66.01	silver quality
vastus lateralis	UBERON:0001379	65.49	gold quality
esophagus squamous epithelium	UBERON:0006920	64.41	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	64.40	gold quality
skeletal muscle tissue	UBERON:0001134	63.84	gold quality
superficial temporal artery	UBERON:0001614	63.51	gold quality
epithelium of mammary gland	UBERON:0003244	63.00	gold quality
mammary duct	UBERON:0001765	62.81	gold quality
cerebellar vermis	UBERON:0004720	62.69	gold quality
cerebellar hemisphere	UBERON:0002245	62.43	gold quality
mucosa of paranasal sinus	UBERON:0005030	62.19	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.42

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• LncRNA LINC01339 Hinders the Development of Wilms’ Tumor via MiR-135b-3p/ADH1C Axis. (PMID:37890508)

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.