CARMN

Summary

CARMN (cardiac mesoderm enhancer-associated non-coding RNA, HGNC:42872) is a long non-coding RNA gene on chromosome 5q32.

Predicted to be involved in regulation of gene expression. Predicted to be part of RISC complex. Biomarker of atherosclerosis.

Source: NCBI Gene 728264 — RefSeq curated summary.

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:42872
Approved symbol	CARMN
Name	cardiac mesoderm enhancer-associated non-coding RNA
Location	5q32
Locus type	RNA, long non-coding
Status	Approved
Aliases	CARMEN
Ensembl gene	ENSG00000249669
Ensembl biotype	lncRNA
OMIM	621305
Entrez	728264
RNAcentral	URS000075B0FB — lncRNA, 1013 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 50 — 50 lncRNA

ENST00000505254, ENST00000505340, ENST00000509909, ENST00000512096, ENST00000518014, ENST00000519898, ENST00000523269, ENST00000524265, ENST00000602315, ENST00000602964, ENST00000614517, ENST00000614896, ENST00000653555, ENST00000655575, ENST00000656891, ENST00000659590, ENST00000660343, ENST00000661249, ENST00000663766, ENST00000686037, ENST00000686110, ENST00000688977, ENST00000691230, ENST00000692133, ENST00000700996, ENST00000850349, ENST00000850350, ENST00000850351, ENST00000850352, ENST00000850353, ENST00000850354, ENST00000850355, ENST00000850356, ENST00000850357, ENST00000850358, ENST00000850359, ENST00000850360, ENST00000850361, ENST00000850362, ENST00000850363, ENST00000850364, ENST00000850365, ENST00000850366, ENST00000850367, ENST00000850368, ENST00000850369, ENST00000850370, ENST00000850371, ENST00000850372, ENST00000850373

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000505254 — 6 exons

Exon	Start	End
ENSE00002021961	149421481	149421601
ENSE00002056286	149415521	149415917
ENSE00002059962	149406878	149407078
ENSE00002063404	149423186	149423309
ENSE00002078557	149424090	149426394
ENSE00003250392	149427873	149428674

Expression profiles

Bgee: expression breadth ubiquitous, 228 present calls, max score 99.37.

FANTOM5 (CAGE): breadth broad, TPM avg 9.5037 / max 1051.1366, expressed in 737 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
59363	6.0619	695
59364	2.9103	288
59362	0.2948	180
59374	0.1307	54
59366	0.0547	23
59361	0.0513	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right coronary artery	UBERON:0001625	99.37	gold quality
lower esophagus muscularis layer	UBERON:0035833	99.34	gold quality
lower esophagus	UBERON:0013473	99.33	gold quality
mucosa of stomach	UBERON:0001199	99.11	gold quality
body of uterus	UBERON:0009853	99.05	gold quality
muscle layer of sigmoid colon	UBERON:0035805	99.03	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	99.03	gold quality
saphenous vein	UBERON:0007318	98.96	gold quality
urethra	UBERON:0000057	98.89	gold quality
popliteal artery	UBERON:0002250	98.88	gold quality
tibial artery	UBERON:0007610	98.87	gold quality
aorta	UBERON:0000947	98.82	gold quality
thoracic aorta	UBERON:0001515	98.77	gold quality
ascending aorta	UBERON:0001496	98.75	gold quality
myometrium	UBERON:0001296	98.73	gold quality
descending thoracic aorta	UBERON:0002345	98.70	gold quality
left coronary artery	UBERON:0001626	98.59	gold quality
coronary artery	UBERON:0001621	98.42	gold quality
left uterine tube	UBERON:0001303	98.41	gold quality
nipple	UBERON:0002030	98.27	gold quality
seminal vesicle	UBERON:0000998	98.24	gold quality
lower esophagus mucosa	UBERON:0035834	98.17	gold quality
colonic epithelium	UBERON:0000397	98.07	gold quality
cauda epididymis	UBERON:0004360	97.47	gold quality
smooth muscle tissue	UBERON:0001135	97.37	gold quality
endocervix	UBERON:0000458	96.76	gold quality
prostate gland	UBERON:0002367	95.89	gold quality
fundus of stomach	UBERON:0001160	95.77	gold quality
pylorus	UBERON:0001166	95.70	gold quality
trachea	UBERON:0003126	95.51	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-11268	yes	3331.78
E-CURD-119	yes	17.82
E-ANND-3	yes	15.26

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 15)

• CARMEN is a crucial regulator of cardiac cell differentiation and homeostasis. (PMID:26423156)
• lncRNAs MHRT, FENDRR and CARMEN show distinct expression profiles in hypertensive patients (PMID:29917257)
• MiR-143HG Gene Polymorphisms as Risk Factors for Gastric Cancer in Chinese Han Population. (PMID:31880258)
• results of our study suggested that CARMN variations may affect the risk of esophageal cancer (PMID:32305636)
• LncRNA miR143HG inhibits the proliferation of glioblastoma cells by sponging miR-504. (PMID:33461388)
• CARMN Loss Regulates Smooth Muscle Cells and Accelerates Atherosclerosis in Mice. (PMID:33622045)
• LncRNA CARMN overexpression promotes prognosis and chemosensitivity of triple negative breast cancer via acting as miR143-3p host gene and inhibiting DNA replication. (PMID:34162418)
• A Smooth Muscle Cell-Enriched Long Noncoding RNA Regulates Cell Plasticity and Atherosclerosis by Interacting With Serum Response Factor. (PMID:34289702)
• CARMN Is an Evolutionarily Conserved Smooth Muscle Cell-Specific LncRNA That Maintains Contractile Phenotype by Binding Myocardin. (PMID:34694145)
• LncRNA CARMN Affects Hepatocellular Carcinoma Prognosis by Regulating the miR-192-5p/LOXL2 Axis. (PMID:36254230)
• LncRNA CARMN inhibits cervical cancer cell growth via the miR-92a-3p/BTG2/Wnt/beta-catenin axis. (PMID:36314369)
• The Long Noncoding RNA Cardiac Mesoderm Enhancer-Associated Noncoding RNA (Carmn) Is a Critical Regulator of Gastrointestinal Smooth Muscle Contractile Function and Motility. (PMID:37030336)
• LncRNA CARMN facilitates odontogenic differentiation of dental pulp cells by impairing EZH2. (PMID:37222221)
• Post-transcriptional regulation of tumor suppressor gene lncRNA CARMN via m[6]A modification and miRNA regulation in cervical cancer. (PMID:37273106)
• MIR143HG promotes methylation of transcription factor HOXB7 promoter by recruiting methyltransferase DNMT1 to prevent the progression of colon cancer. (PMID:38127104)

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.