LINC00261

Summary

LINC00261 (long intergenic non-protein coding RNA 261, HGNC:16189) is a long non-coding RNA gene on chromosome 20p11.21.

This gene produces a long non-coding RNA that acts as a negative regulator of cell growth. This transcript may promote differentiation and apoptosis.

Source: NCBI Gene 140828 — RefSeq curated summary.

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:16189
Approved symbol	LINC00261
Name	long intergenic non-protein coding RNA 261
Location	20p11.21
Locus type	RNA, long non-coding
Status	Approved
Aliases	bA216C10.1, HCCDR1, TCONS_00027846, ALIEN, DEANR1, onco-lncRNA-17, FALCOR, LCAL62
Ensembl gene	ENSG00000259974
Ensembl biotype	lncRNA
OMIM	618518
Entrez	140828
RNAcentral	URS000075C45D — lncRNA, 4924 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 lncRNA

ENST00000420070, ENST00000564492, ENST00000609300, ENST00000697618, ENST00000697619, ENST00000697620, ENST00000697621, ENST00000702241, ENST00000821803, ENST00000821804, ENST00000821805, ENST00000821806

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000420070 — 4 exons

Exon	Start	End
ENSE00001680660	22548848	22548951
ENSE00001683780	22560770	22560924
ENSE00001713967	22548402	22548497
ENSE00003971205	22547671	22548110

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 97.37.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 4.9080 / max 1161.0182, expressed in 181 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
186634	4.8548	180
186635	0.0532	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	97.37	gold quality
liver	UBERON:0002107	96.73	gold quality
fundus of stomach	UBERON:0001160	95.17	gold quality
body of pancreas	UBERON:0001150	93.79	gold quality
pancreas	UBERON:0001264	92.13	gold quality
pylorus	UBERON:0001166	91.97	gold quality
islet of Langerhans	UBERON:0000006	90.51	gold quality
mucosa of sigmoid colon	UBERON:0004993	90.03	gold quality
stomach	UBERON:0000945	89.93	gold quality
body of stomach	UBERON:0001161	89.76	gold quality
cardia of stomach	UBERON:0001162	89.24	gold quality
rectum	UBERON:0001052	88.02	gold quality
tibia	UBERON:0000979	86.99	gold quality
epithelial cell of pancreas	CL:0000083	85.46	silver quality
ileal mucosa	UBERON:0000331	84.86	silver quality
colonic mucosa	UBERON:0000317	84.78	gold quality
gall bladder	UBERON:0002110	84.59	gold quality
duodenum	UBERON:0002114	83.27	gold quality
pancreatic ductal cell	CL:0002079	79.10	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.13	silver quality
colonic epithelium	UBERON:0000397	77.88	gold quality
mucosa of transverse colon	UBERON:0004991	77.23	gold quality
transverse colon	UBERON:0001157	75.38	gold quality
large intestine	UBERON:0000059	72.57	gold quality
intestine	UBERON:0000160	72.24	gold quality
colon	UBERON:0001155	71.73	gold quality
small intestine	UBERON:0002108	71.26	gold quality
small intestine Peyer’s patch	UBERON:0003454	69.72	gold quality
right lung	UBERON:0002167	69.48	gold quality
jejunal mucosa	UBERON:0000399	68.15	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.82

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 27)

• ALIEN, is specifically expressed in cardiovascular progenitors. Its knockdown upregulated 738 genes involved in cell adhesion and extracellular matrix remodeling, and downregulated 503 genes related to angiogenesis. (PMID:25739401)
• DEANR1 facilitates FOXA2 activation by facilitating SMAD2/3 recruitment to the FOXA2 promoter (PMID:25843708)
• linc00261 acts a tumour suppressor in Gastric cancer by decreasing the stability of Slug proteins and suppressing epithelial-mesenchymal transition. (PMID:27878953)
• our data show that the lncRNA LINC00261 was significantly downregulated in choriocarcinoma tissues and cell lines. Overexpression of LINC00261 suppresses the cell proliferation, migration, and invasion abilities in choriocarcinoma. (PMID:27983929)
• LINC00261 inhibits cell growth and migration in endometriosis. (PMID:28707780)
• we also demonstrated that upregulation of LINC00261 significantly inhibited Notch signaling by downregulating Notch1 and Hes-1 expression in HCC cells. (PMID:29278875)
• LINC00261 promotes FOXO1 expression through reducing FOXO1-targeted miRNAs to suppress endometrial carcinoma cell proliferation, migration, and invasion. (PMID:30019459)
• the results of the study provided evidence emphasizing the distinct antitumor ability of LINC00261 in cases of esophageal cancer, which was manifested by overexpression of LINC00261 detected to increase the sensitivity of human esophageal cancer cells to 5-FU by mediating methylation-dependent repression of DPYD. (PMID:30226808)
• Linc00261 may serve as a new prognostic biomarker for predicting the postoperative outcomes of the patients with hepatocellular carcinoma. (PMID:30377132)
• Upregulated long noncoding RNA Linc00261 in pre-eclampsia and its effect on trophoblast invasion and migration via regulating miR-558/TIMP4 signaling pathway. (PMID:30891826)
• LINC00261 represses colon cancer progression by regulating miR-324-3p expression and activity of the Wnt pathway. (PMID:31183860)
• Up-regulated LINC00261 predicts a poor prognosis and promotes a metastasis by EMT process in cholangiocarcinoma. (PMID:31812439)
• Data indicate that long intergenic non-protein coding RNA 261 (LINC00261) might be used as a molecular biomarker for evaluating the metastasis and recurrence-free survival of colon cancer. (PMID:31850713)
• Linc00261 inhibits metastasis and the WNT signaling pathway of pancreatic cancer by regulating a miR5525p/FOXO3 axis. (PMID:32020223)
• LINC00261 inhibits progression of pancreatic cancer by down-regulating miR-23a-3p. (PMID:32590069)
• Methylation-mediated LINC00261 suppresses pancreatic cancer progression by epigenetically inhibiting c-Myc transcription. (PMID:32929371)
• Reconstruction of lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveals functional lncRNAs in skin cutaneous melanoma. (PMID:32993558)
• Epigenetic silencing of LncRNA LINC00261 promotes c-myc-mediated aerobic glycolysis by regulating miR-222-3p/HIPK2/ERK axis and sequestering IGF2BP1. (PMID:33122827)
• LINC00261/microRNA-550a-3p/SDPR axis affects the biological characteristics of breast cancer stem cells. (PMID:33274565)
• Identification of the 3-lncRNA Signature as a Prognostic Biomarker for Colorectal Cancer. (PMID:33302562)
• LINC00261 relieves the progression of sepsis-induced acute kidney injury by inhibiting NF-kappaB activation through targeting the miR-654-5p/SOCS3 axis. (PMID:33481135)
• The evolutionarily conserved long non-coding RNA LINC00261 drives neuroendocrine prostate cancer proliferation and metastasis via distinct nuclear and cytoplasmic mechanisms. (PMID:33793068)
• LINC00261 elevation inhibits angiogenesis and cell cycle progression of pancreatic cancer cells by upregulating SCP2 via targeting FOXP3. (PMID:34541823)
• LINC00261 regulates EBF1 to suppress malignant progression of thyroid cancer. (PMID:34982424)
• TGF-beta1 induced deficiency of linc00261 promotes epithelial-mesenchymal-transition and stemness of hepatocellular carcinoma via modulating SMAD3. (PMID:35123494)
• The LINC00261/MiR105-5p/SELL axis is involved in dysfunction of B cell and is associated with overall survival in hepatocellular carcinoma. (PMID:35702258)
• The CDK1-Related lncRNA and CXCL8 Mediated Immune Resistance in Lung Adenocarcinoma. (PMID:36078096)

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.