NPTN-IT1

Summary

NPTN-IT1 (NPTN intronic transcript 1, HGNC:45091) is a long non-coding RNA gene on chromosome 15q24.1.

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:45091
Approved symbol	NPTN-IT1
Name	NPTN intronic transcript 1
Location	15q24.1
Locus type	RNA, long non-coding
Status	Approved
Aliases	lncRNA-LET
Ensembl gene	ENSG00000281183
Ensembl biotype	lncRNA
OMIM	615176
Entrez	101241892
RNAcentral	URS000075EF67 — lncRNA, 2606 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 lncRNA

ENST00000628401

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000628401 — 1 exons

Exon	Start	End
ENSE00003773477	73567012	73569294

Expression profiles

Bgee: expression breadth ubiquitous, 247 present calls, max score 94.85.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2692 / max 4.8291, expressed in 117 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
150852	0.2692	117

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
nipple	UBERON:0002030	94.85	gold quality
cardiac muscle of right atrium	UBERON:0003379	94.20	silver quality
middle temporal gyrus	UBERON:0002771	93.74	gold quality
buccal mucosa cell	CL:0002336	93.40	gold quality
Brodmann (1909) area 23	UBERON:0013554	93.39	gold quality
left ventricle myocardium	UBERON:0006566	93.38	gold quality
pylorus	UBERON:0001166	91.13	gold quality
urethra	UBERON:0000057	91.12	gold quality
endothelial cell	CL:0000115	90.83	gold quality
trachea	UBERON:0003126	90.79	gold quality
tendon of biceps brachii	UBERON:0008188	90.66	gold quality
oviduct epithelium	UBERON:0004804	90.54	gold quality
cerebellar vermis	UBERON:0004720	90.37	gold quality
visceral pleura	UBERON:0002401	90.30	gold quality
upper arm skin	UBERON:0004263	90.19	gold quality
cardia of stomach	UBERON:0001162	89.86	gold quality
lateral nuclear group of thalamus	UBERON:0002736	89.74	gold quality
lateral globus pallidus	UBERON:0002476	89.73	gold quality
postcentral gyrus	UBERON:0002581	89.48	gold quality
sperm	CL:0000019	88.89	gold quality
parietal lobe	UBERON:0001872	88.82	gold quality
tibialis anterior	UBERON:0001385	88.71	gold quality
tibia	UBERON:0000979	88.58	gold quality
penis	UBERON:0000989	88.52	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.43	gold quality
renal medulla	UBERON:0000362	87.15	gold quality
superior frontal gyrus	UBERON:0002661	87.04	gold quality
saphenous vein	UBERON:0007318	87.00	gold quality
pharyngeal mucosa	UBERON:0000355	86.78	gold quality
adult organism	UBERON:0007023	86.49	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.51

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 5)

• The role of lncRNA-LET as a regulator of hypoxia signaling in hepatocellular carcinoma. (PMID:23395002)
• lncRNA-LET exhibits an important tumor-suppressive effect on Lung Adenocarcinoma progression by inhibiting EMT and Wnt/beta-catenin pathway, which provides potential therapeutic targets for Lung Adenocarcinoma. (PMID:27896272)
• Decreased lncRNA LET expression was detected in burn tissues compared with normal skin. (PMID:29393360)
• Overexpression of lncRNA-LET inhibits cell viability, migration and EMT process, and increases apoptosis in KGN cells. (PMID:29432996)
• The expression of lncRNA LET was reduced in breast cancer tissues and MDA-MB-231 cell line. lncRNA LET expression plays a key role in the proliferation, invasion and migration of breast cancer cells. It is a new type of molecule involved in the development of breast cancer. (PMID:30280783)

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.