FOXCUT

Summary

FOXCUT (FOXC1 upstream transcript, HGNC:50650) is a long non-coding RNA gene on chromosome 6p25.3.

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:50650
Approved symbol	FOXCUT
Name	FOXC1 upstream transcript
Location	6p25.3
Locus type	RNA, long non-coding
Status	Approved
Aliases	TCONS_00011636
Ensembl gene	ENSG00000280916
Ensembl biotype	lncRNA
OMIM	615976
Entrez	101927703
RNAcentral	URS00007E4B8E — lncRNA, 1612 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 lncRNA

ENST00000628509, ENST00000652712, ENST00000688683, ENST00000841110, ENST00000841111, ENST00000841112, ENST00000841113

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000628509 — 2 exons

Exon	Start	End
ENSE00003762652	1606016	1606079
ENSE00003764463	1605531	1605799

Expression profiles

Bgee: expression breadth ubiquitous, 143 present calls, max score 92.19.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0648 / max 36.3832, expressed in 12 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
65427	0.0648	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
descending thoracic aorta	UBERON:0002345	92.19	gold quality
thoracic aorta	UBERON:0001515	90.83	gold quality
ascending aorta	UBERON:0001496	90.72	gold quality
upper arm skin	UBERON:0004263	90.33	gold quality
epithelial cell of pancreas	CL:0000083	87.12	gold quality
aorta	UBERON:0000947	85.84	gold quality
popliteal artery	UBERON:0002250	82.20	gold quality
tibial artery	UBERON:0007610	82.19	gold quality
pancreatic ductal cell	CL:0002079	80.68	silver quality
saliva-secreting gland	UBERON:0001044	80.40	gold quality
minor salivary gland	UBERON:0001830	79.28	gold quality
tibialis anterior	UBERON:0001385	79.22	silver quality
vena cava	UBERON:0004087	77.54	gold quality
mouth mucosa	UBERON:0003729	77.34	gold quality
bone marrow cell	CL:0002092	77.21	gold quality
caecum	UBERON:0001153	76.79	gold quality
pharyngeal mucosa	UBERON:0000355	76.54	gold quality
cardia of stomach	UBERON:0001162	76.49	gold quality
layer of synovial tissue	UBERON:0007616	75.73	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.65	gold quality
pericardium	UBERON:0002407	75.38	silver quality
trachea	UBERON:0003126	75.38	gold quality
body of tongue	UBERON:0011876	75.11	gold quality
coronary artery	UBERON:0001621	75.03	gold quality
adult mammalian kidney	UBERON:0000082	74.96	gold quality
left coronary artery	UBERON:0001626	74.96	gold quality
right coronary artery	UBERON:0001625	74.70	gold quality
nipple	UBERON:0002030	74.61	gold quality
saphenous vein	UBERON:0007318	74.50	gold quality
thymus	UBERON:0002370	74.38	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.11

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 10)

• Report lncRNA FOXC1 upstream transcript (FOXCUT) overexpressed in oral squamous cell carcinoma. (PMID:24889262)
• Our findings suggested that FOXCUT expression contributed to the development and progression of nasopharyngeal carcinoma by targeting FOXC1 and that FOXCUT might be useful as a potential nasopharyngeal carcinoma biomarker and therapeutic target. (PMID:28635400)
• data indicated that MMP-2/MMP-9 was coordinately targeted by two non-coding RNAs, miR-296-3p and FOXCUT, which were decreased, and tumor-suppressing factors in choroidal malignant melanoma (PMID:29260433)
• Verification of expressions of lncRNA FOXCUT in gastric adenocarcinoma patients and its effects on cell biological function based on TCGA database. (PMID:31364114)
• Over expression of lncRNA FOXCUT is detected in the early stages of prostate cancer and correlates with poor prognosis. (PMID:31710451)
• LncRNA FOXCUT Stimulates the Progression of Endometrial Cancer. (PMID:34591391)
• [Interference of long noncoding RNA FOXCUT inhibits epithelial-mesenchymal transformation and induces mitochondrial injury in nasopharyngeal carcinoma cells]. (PMID:34658347)
• Serum lncRNAs, NBAT-1, and FOXCUT signature in hepatocellular carcinoma developed on top of chronic hepatitis C. (PMID:36440815)
• Promotion effect of FOXCUT as a microRNA sponge for miR-24-3p on progression in triple-negative breast cancer through the p38 MAPK signaling pathway. (PMID:38178324)
• FOXCUT regulates the malignant phenotype of triple-negative breast Cancer via the miR-337-3p/ANP32E Axis. (PMID:38944356)

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.