GACAT3

Summary

GACAT3 (gastric cancer associated transcript 3, HGNC:50847) is a long non-coding RNA gene on chromosome 2p24.3.

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:50847
Approved symbol	GACAT3
Name	gastric cancer associated transcript 3
Location	2p24.3
Locus type	RNA, long non-coding
Status	Approved
Aliases	lncRNA-AC130710
Ensembl gene	ENSG00000236289
Ensembl biotype	lncRNA
OMIM	616132
Entrez	104797537
RNAcentral	URS00007E409E — lncRNA, 984 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 21 lncRNA

ENST00000426539, ENST00000442387, ENST00000651705, ENST00000651908, ENST00000651993, ENST00000652394, ENST00000652731, ENST00000667080, ENST00000777279, ENST00000777280, ENST00000777281, ENST00000777282, ENST00000777283, ENST00000777284, ENST00000777285, ENST00000777286, ENST00000777287, ENST00000777288, ENST00000777289, ENST00000777290, ENST00000777291

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000426539 — 4 exons

Exon	Start	End
ENSE00001603503	16050427	16050677
ENSE00001641159	16085289	16085801
ENSE00001706921	16073304	16073442
ENSE00001799252	16080898	16081090

Expression profiles

Bgee: expression breadth broad, 92 present calls, max score 96.28.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0835 / max 16.1639, expressed in 19 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
19018	0.0835	19

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	96.28	gold quality
quadriceps femoris	UBERON:0001377	94.46	gold quality
thymus	UBERON:0002370	75.49	silver quality
bone marrow	UBERON:0002371	74.12	silver quality
skeletal muscle tissue	UBERON:0001134	71.94	silver quality
spinal cord	UBERON:0002240	62.25	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	62.22	gold quality
ganglionic eminence	UBERON:0004023	60.56	gold quality
ventricular zone	UBERON:0003053	59.46	silver quality
primary visual cortex	UBERON:0002436	58.58	gold quality
sural nerve	UBERON:0015488	57.22	silver quality
substantia nigra	UBERON:0002038	57.03	gold quality
prefrontal cortex	UBERON:0000451	56.85	gold quality
right adrenal gland cortex	UBERON:0035827	55.88	gold quality
spleen	UBERON:0002106	54.01	gold quality
heart left ventricle	UBERON:0002084	53.78	gold quality
monocyte	CL:0000576	53.13	gold quality
urinary bladder	UBERON:0001255	53.03	silver quality
right adrenal gland	UBERON:0001233	52.79	gold quality
frontal cortex	UBERON:0001870	51.48	gold quality
adrenal tissue	UBERON:0018303	51.18	gold quality
minor salivary gland	UBERON:0001830	51.13	gold quality
liver	UBERON:0002107	50.82	silver quality
Ammon’s horn	UBERON:0001954	50.65	gold quality
blood	UBERON:0000178	50.64	gold quality
left ovary	UBERON:0002119	50.50	gold quality
adrenal gland	UBERON:0002369	50.45	gold quality
ovary	UBERON:0000992	50.35	gold quality
superior frontal gyrus	UBERON:0002661	49.87	gold quality
left adrenal gland cortex	UBERON:0035825	49.74	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.61

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 9)

• lncRNA-AC130710 may be a potential tumor marker for gastric cancer prognosis (PMID:24969565)
• Studies suggest that GACAT2 (long noncoding RNA HMlincRNA717) and GACAT3 (long noncoding RNA AC130710) may play crucial roles in the occurrence, development and diagnosis of gastric carcinoma. (PMID:25077925)
• as a downstream target of the IL6/STAT3 signaling, Long non-coding RNA GACAT3 promotes gastric cancer cell growth suggesting that GACAT3 is an inflammatory response gene and may be served as a valuable potential target for the treatment of gastric cancer. (PMID:27644247)
• GACAT3 promotes breast cancer malignancy by sponging miR-497, leading to the enhancement of its endogenous target CCND2. These results suggest that GACAT3/miR-497/CCND2 is a potential therapeutic target and biomarker for breast cancer (PMID:29945347)
• Study demonstrate that GACAT3 acts as a competing endogenous RNA of HMGA1. Its knockdown resulted in significantly decreased cell proliferation of gastric cancer cells, similar to the effect of an HMGA1 knockdown. (PMID:30098426)
• This study elucidated that GACAT3/miR-3127-5p/ELAVL1 signaling regulates glioma development and might be a promising therapeutic target. (PMID:30317610)
• Long noncoding RNA GACAT3 regulates the expression of NAMPT to promote glioma progression by sponging miR-135a. (PMID:30536379)
• High LncRNA-GACAT3 expression is associated with breast cancer. (PMID:31983109)
• LncRNAs GACAT3 and LINC00152 regulate each other through miR-103 and are associated with clinicopathological characteristics in colorectal cancer. (PMID:32462718)

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.