LETR1

Summary

LETR1 (lymphatic endothelial transcriptional regulator lncRNA 1, HGNC:49597) is a long non-coding RNA gene on chromosome 15q26.2.

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:49597
Approved symbol	LETR1
Name	lymphatic endothelial transcriptional regulator lncRNA 1
Location	15q26.2
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000248441
Ensembl biotype	lncRNA
OMIM	621297
Entrez	400456
RNAcentral	URS000075C35D — lncRNA, 1445 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 48 — 48 lncRNA

ENST00000508732, ENST00000555332, ENST00000556899, ENST00000611265, ENST00000614853, ENST00000653272, ENST00000654052, ENST00000655274, ENST00000656019, ENST00000658041, ENST00000658123, ENST00000659002, ENST00000659107, ENST00000659343, ENST00000660741, ENST00000661153, ENST00000661491, ENST00000662295, ENST00000663436, ENST00000664127, ENST00000664421, ENST00000665255, ENST00000670445, ENST00000670739, ENST00000689353, ENST00000698229, ENST00000698230, ENST00000698231, ENST00000698232, ENST00000698249, ENST00000698250, ENST00000698251, ENST00000698252, ENST00000698253, ENST00000698309, ENST00000698310, ENST00000698311, ENST00000698312, ENST00000698313, ENST00000698314, ENST00000698315, ENST00000698316, ENST00000701331, ENST00000701654, ENST00000703417, ENST00000840798, ENST00000840799, ENST00000840800

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000508732 — 4 exons

Exon	Start	End
ENSE00002026268	95288302	95288468
ENSE00002062627	95279284	95280096
ENSE00002079204	95326830	95327100
ENSE00003973263	95289422	95289554

Expression profiles

Bgee: expression breadth ubiquitous, 155 present calls, max score 90.67.

FANTOM5 (CAGE): breadth broad, TPM avg 1.4193 / max 172.2434, expressed in 323 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
151683	0.6539	221
151685	0.3774	207
151684	0.2036	134
151686	0.1845	107

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibial artery	UBERON:0007610	90.67	gold quality
popliteal artery	UBERON:0002250	90.65	gold quality
left ovary	UBERON:0002119	90.37	gold quality
right coronary artery	UBERON:0001625	89.76	gold quality
sural nerve	UBERON:0015488	89.46	gold quality
right ovary	UBERON:0002118	88.18	gold quality
tibial nerve	UBERON:0001323	87.75	gold quality
left coronary artery	UBERON:0001626	87.63	gold quality
calcaneal tendon	UBERON:0003701	85.47	gold quality
coronary artery	UBERON:0001621	85.25	gold quality
aorta	UBERON:0000947	83.40	gold quality
ovary	UBERON:0000992	82.09	gold quality
left uterine tube	UBERON:0001303	79.25	gold quality
spleen	UBERON:0002106	78.44	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.31	gold quality
omental fat pad	UBERON:0010414	78.26	gold quality
peritoneum	UBERON:0002358	78.16	gold quality
gall bladder	UBERON:0002110	77.53	gold quality
body of uterus	UBERON:0009853	76.77	gold quality
adipose tissue of abdominal region	UBERON:0007808	76.21	gold quality
endocervix	UBERON:0000458	75.70	gold quality
anterior cingulate cortex	UBERON:0009835	75.36	gold quality
metanephros cortex	UBERON:0010533	75.36	gold quality
ascending aorta	UBERON:0001496	74.64	gold quality
subcutaneous adipose tissue	UBERON:0002190	74.53	gold quality
thoracic aorta	UBERON:0001515	74.33	gold quality
right lobe of thyroid gland	UBERON:0001119	74.18	gold quality
cortical plate	UBERON:0005343	73.82	gold quality
Brodmann (1909) area 9	UBERON:0013540	73.71	gold quality
colonic epithelium	UBERON:0000397	73.67	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	16.92
E-ANND-3	yes	5.50

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 5)

• The novel FOXO1/LINC01197/b-catenin axis was dysregulated during pancreatic ductal adenocarcinoma (PDAC)progression. Our study provides insight into the mechanisms of LINC01197 in PDAC and reveal a potential target for PDAC clinical therapy and prognostic prediction. (PMID:31027497)
• Clinical significance of CA 19.9 and LINC01197 in pancreatic cancer. (PMID:32196587)
• LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C. (PMID:33568674)
• LncRNA LINC01197 inhibited the formation of calcium oxalate-induced kidney stones by regulating miR-516b-5p/SIRT3/FOXO1 signaling pathway. (PMID:36688989)
• LINC01197 inhibits influenza A virus replication by serving as a PABPC1 decoy. (PMID:39334466)

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.