NALT1

Summary

NALT1 (NOTCH1 associated lncRNA in T cell acute lymphoblastic leukemia 1, HGNC:51192) is a long non-coding RNA gene on chromosome 9q34.3.

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:51192
Approved symbol	NALT1
Name	NOTCH1 associated lncRNA in T cell acute lymphoblastic leukemia 1
Location	9q34.3
Locus type	RNA, long non-coding
Status	Approved
Aliases	TCONS_l2_00029132
Ensembl gene	ENSG00000237886
Ensembl biotype	lncRNA
Entrez	101928483
RNAcentral	URS000075D3F1 — lncRNA, 546 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 48 — 48 lncRNA

ENST00000429224, ENST00000450304, ENST00000701978, ENST00000743454, ENST00000743455, ENST00000743456, ENST00000743457, ENST00000743458, ENST00000743459, ENST00000743460, ENST00000743461, ENST00000743462, ENST00000743463, ENST00000743464, ENST00000743465, ENST00000743466, ENST00000743467, ENST00000743468, ENST00000743469, ENST00000743470, ENST00000743471, ENST00000743472, ENST00000743473, ENST00000743474, ENST00000743475, ENST00000743476, ENST00000743477, ENST00000743478, ENST00000743479, ENST00000743480, ENST00000743481, ENST00000743482, ENST00000743483, ENST00000743484, ENST00000743485, ENST00000743486, ENST00000743487, ENST00000743488, ENST00000743489, ENST00000743490, ENST00000743491, ENST00000743492, ENST00000743493, ENST00000743494, ENST00000743495, ENST00000743496, ENST00000743497, ENST00000743498

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000429224 — 3 exons

Exon	Start	End
ENSE00001753291	136547842	136548101
ENSE00004081908	136546190	136546371
ENSE00004081929	136549132	136549749

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 94.87.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1062 / max 27.0103, expressed in 32 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
99510	0.0636	24
99511	0.0426	13

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
muscle layer of sigmoid colon	UBERON:0035805	94.87	gold quality
lower esophagus muscularis layer	UBERON:0035833	93.84	gold quality
lower esophagus	UBERON:0013473	93.79	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	93.42	gold quality
mucosa of stomach	UBERON:0001199	89.48	gold quality
right uterine tube	UBERON:0001302	83.50	gold quality
body of uterus	UBERON:0009853	83.48	gold quality
esophagus	UBERON:0001043	83.37	gold quality
colonic epithelium	UBERON:0000397	82.49	gold quality
left uterine tube	UBERON:0001303	82.28	gold quality
transverse colon	UBERON:0001157	82.02	gold quality
lower esophagus mucosa	UBERON:0035834	80.89	gold quality
endocervix	UBERON:0000458	80.57	gold quality
popliteal artery	UBERON:0002250	80.53	gold quality
tibial artery	UBERON:0007610	80.52	gold quality
colon	UBERON:0001155	79.99	gold quality
aorta	UBERON:0000947	79.74	gold quality
fundus of stomach	UBERON:0001160	79.49	gold quality
left lobe of thyroid gland	UBERON:0001120	79.35	gold quality
ascending aorta	UBERON:0001496	79.14	gold quality
descending thoracic aorta	UBERON:0002345	79.11	gold quality
right lobe of thyroid gland	UBERON:0001119	79.05	gold quality
thoracic aorta	UBERON:0001515	79.03	gold quality
smooth muscle tissue	UBERON:0001135	79.01	gold quality
left coronary artery	UBERON:0001626	78.68	gold quality
large intestine	UBERON:0000059	78.60	gold quality
thyroid gland	UBERON:0002046	78.25	gold quality
right coronary artery	UBERON:0001625	77.90	gold quality
intestine	UBERON:0000160	77.45	gold quality
small intestine Peyer’s patch	UBERON:0003454	77.34	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.88

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• a neighbor of NOTCH1, Lnc-RP11-611D20.2 (named NALT) which could regulate the NOTCH1 signal pathway through cis-regulation, was identified. (PMID:26330272)
• NALT1 was overexpressed in gastric cancer (GC) and promoted invasion and metastasis of GC. The over-expression of NALT1 was linked to poor prognosis in GC. The mechanism may be related to the regulation of NOTCH1 by NALT1 and its effect on the expression of NOTCH signaling pathway. (PMID:31802831)
• LncRNA NALT1 promotes colorectal cancer progression via targeting PEG10 by sponging microRNA-574-5p. (PMID:36385135)

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.