LNCNEF

Summary

LNCNEF (lncRNA neighboring enhancer of FOXA2, HGNC:50656) is a long non-coding RNA gene on chromosome 20p11.21.

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:50656
Approved symbol	LNCNEF
Name	lncRNA neighboring enhancer of FOXA2
Location	20p11.21
Locus type	RNA, long non-coding
Status	Approved
Aliases	lncRNA-NEF
Ensembl gene	ENSG00000237396
Ensembl biotype	lncRNA
Entrez	101929685
RNAcentral	URS000075C152 — lncRNA, 675 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 lncRNA

ENST00000422494, ENST00000797275

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000422494 — 3 exons

Exon	Start	End
ENSE00001716210	22589192	22589411
ENSE00004183767	22607346	22607856
ENSE00004183769	22587517	22587788

Expression profiles

Bgee: expression breadth broad, 37 present calls, max score 66.20.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left lobe of thyroid gland	UBERON:0001120	66.20	gold quality
thyroid gland	UBERON:0002046	65.46	gold quality
right lobe of thyroid gland	UBERON:0001119	64.37	gold quality
endometrium	UBERON:0001295	60.87	gold quality
multicellular organism	UBERON:0000468	57.51	gold quality
monocyte	CL:0000576	54.38	gold quality
calcaneal tendon	UBERON:0003701	54.27	gold quality
islet of Langerhans	UBERON:0000006	49.95	gold quality
fundus of stomach	UBERON:0001160	47.35	gold quality
body of pancreas	UBERON:0001150	44.42	silver quality
heart left ventricle	UBERON:0002084	44.39	silver quality
gastrocnemius	UBERON:0001388	44.18	silver quality
lower esophagus muscularis layer	UBERON:0035833	43.99	silver quality
right lobe of liver	UBERON:0001114	43.68	silver quality
blood	UBERON:0000178	43.46	silver quality
muscle layer of sigmoid colon	UBERON:0035805	43.27	silver quality
lung	UBERON:0002048	42.47	gold quality
colon	UBERON:0001155	41.97	silver quality
ascending aorta	UBERON:0001496	41.34	silver quality
stomach	UBERON:0000945	41.27	silver quality
transverse colon	UBERON:0001157	40.50	silver quality
adenohypophysis	UBERON:0002196	40.28	silver quality
body of stomach	UBERON:0001161	40.25	silver quality
tibial artery	UBERON:0007610	39.65	silver quality
subcutaneous adipose tissue	UBERON:0002190	39.56	silver quality
fallopian tube	UBERON:0003889	39.29	silver quality
minor salivary gland	UBERON:0001830	39.21	silver quality
Ammon’s horn	UBERON:0001954	39.02	silver quality
caudate nucleus	UBERON:0001873	37.99	silver quality
right atrium auricular region	UBERON:0006631	37.93	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.47

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 5)

• LncRNA-NEF regulates epithelial-mesenchymal transition and cancer metastasis via cis-regulating FOXA2. (PMID:29311643)
• Serum NEF is a sensitive diagnostic and prognostic marker for gastric carcinoma. NEF siRNA silencing promoted, and overexpression inhibited, gastric carcinoma proliferation. In addition, NEF overexpression promoted, and NEF siRNA silencing inhibited, Runx1 expression. Therefore, it was concluded that lncRNA NEF may participate in the regulation of cancer cell proliferation by regulating Runx1 expression (PMID:30664208)
• Plasma levels LncRNA and miRNA-155 were inversely correlated in triple-negative breast cancer (TNBC) patients. (PMID:30839051)
• lncRNA-NEF participated in intrahepatic cholangiocarcinoma possibly by interacting with RUNX1. (PMID:31015363)
• Overexpression of lncRNA-NEF regulates the miR-155/PTEN axis to inhibit adipogenesis and promote osteogenesis. (PMID:34382731)

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.