LINC00339

Summary

LINC00339 (long intergenic non-protein coding RNA 339, HGNC:25011) is a long non-coding RNA gene on chromosome 1p36.12.

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:25011
Approved symbol	LINC00339
Name	long intergenic non-protein coding RNA 339
Location	1p36.12
Locus type	RNA, long non-coding
Status	Approved
Aliases	HSPC157
Ensembl gene	ENSG00000218510
Ensembl biotype	lncRNA
Entrez	29092
RNAcentral	URS000075D5F9 — lncRNA, 1206 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 lncRNA

ENST00000404210, ENST00000416769, ENST00000420503, ENST00000434233, ENST00000452322, ENST00000634451, ENST00000634712, ENST00000634934, ENST00000635450, ENST00000635675, ENST00000641009, ENST00000642072

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000404210 — 3 exons

Exon	Start	End
ENSE00001666669	22030280	22031223
ENSE00001728593	22025532	22025643
ENSE00003813515	22028528	22028660

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 97.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.0028 / max 126.5554, expressed in 1789 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
1266	13.0028	1789
1267	0.8313	549
1268	0.6235	307

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of pancreas	UBERON:0001150	97.24	gold quality
pancreas	UBERON:0001264	93.86	gold quality
right uterine tube	UBERON:0001302	92.07	gold quality
apex of heart	UBERON:0002098	91.18	gold quality
spleen	UBERON:0002106	88.49	gold quality
lymph node	UBERON:0000029	88.26	gold quality
granulocyte	CL:0000094	88.16	gold quality
right lobe of thyroid gland	UBERON:0001119	88.11	gold quality
islet of Langerhans	UBERON:0000006	87.98	gold quality
fallopian tube	UBERON:0003889	87.68	gold quality
leukocyte	CL:0000738	87.55	gold quality
monocyte	CL:0000576	87.51	gold quality
thyroid gland	UBERON:0002046	87.28	gold quality
left lobe of thyroid gland	UBERON:0001120	87.21	gold quality
subcutaneous adipose tissue	UBERON:0002190	87.14	gold quality
left ovary	UBERON:0002119	87.07	gold quality
gall bladder	UBERON:0002110	87.05	gold quality
rectum	UBERON:0001052	86.90	gold quality
adipose tissue	UBERON:0001013	86.73	gold quality
ovary	UBERON:0000992	86.71	gold quality
right lobe of liver	UBERON:0001114	86.64	gold quality
pituitary gland	UBERON:0000007	86.48	gold quality
omental fat pad	UBERON:0010414	86.24	gold quality
endometrium	UBERON:0001295	86.18	gold quality
thoracic mammary gland	UBERON:0005200	86.15	gold quality
metanephros cortex	UBERON:0010533	86.13	gold quality
fundus of stomach	UBERON:0001160	86.08	gold quality
right ovary	UBERON:0002118	86.07	gold quality
smooth muscle tissue	UBERON:0001135	86.06	gold quality
right adrenal gland	UBERON:0001233	85.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.31

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 13)

• Chromatin conformation capture provides evidence for risk SNPs interacting with the promoters of both LINC00339 and CDC4 and luciferase reporter assays suggest the risk SNP rs12038474 is located in a transcriptional silencer for CDC42 and the risk allele increases expression of CDC42. (PMID:28171565)
• Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. (PMID:29706346)
• Results showed that LINC00339 was significantly up-regulated in NSCLC tissue and cells, which indicated the poor prognosis of NSCLC patients. (PMID:29906749)
• LINC00339 regulates ROCK1 by miR-152 to promote cell proliferation and migration in hepatocellular carcinoma. (PMID:31081143)
• LINC00339 was markedly over-expressed in pancreatic cancer (PANC) tissues and cells and promoted cell proliferation, invasion, and migration via sponging miR-497-5p, thereby increasing IGF1R expression. Our study could provide a novel target for PANC diagnosis and biotherapy. (PMID:31128030)
• LINC00339 promotes proliferation, and suppresses apoptosis of colorectal cancer cells via downregulating miR-218 (PMID:31269584)
• LINC00339 regulated ovarian cancer cell proliferation, migration, and invasion by targeting miR-148a-3p/ROCK1 pathway. (PMID:31550677)
• Avasimibe inhibits the proliferation, migration and invasion of glioma cells by suppressing linc00339. (PMID:32682982)
• CCL18-induced LINC00319 promotes proliferation and metastasis in oral squamous cell carcinoma via the miR-199a-5p/FZD4 axis. (PMID:32948745)
• Elucidating the role of long intergenic non-coding RNA 339 in human endometrium and endometriosis. (PMID:33576410)
• LINC00339: An emerging major player in cancer and metabolic diseases. (PMID:35276468)
• LINC00339 accelerates invasion and migration of colorectal cancer via mediating miRNA-30a-5p. (PMID:38279428)
• Functional mechanism and clinical implications of LINC00339 in delayed fracture healing. (PMID:39192334)

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.