LINC00941

Summary

LINC00941 (long intergenic non-protein coding RNA 941, HGNC:48635) is a long non-coding RNA gene on chromosome 12p11.21.

Enables promoter-enhancer loop anchoring activity. Involved in chromatin looping and positive regulation of transcription by RNA polymerase II.

Source: NCBI Gene 100287314 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 3 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:48635
Approved symbol	LINC00941
Name	long intergenic non-protein coding RNA 941
Location	12p11.21
Locus type	RNA, long non-coding
Status	Approved
Aliases	LISRR, lncRNA-MUF, lncIAPF
Ensembl gene	ENSG00000235884
OMIM	620799
Entrez	100287314
RNAcentral	URS000075A607 — lncRNA, 1895 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 0

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

None — 0 exons

Expression profiles

Bgee: expression breadth broad, 68 present calls, max score 77.22.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.22	silver quality
muscle tissue	UBERON:0002385	71.04	gold quality
vermiform appendix	UBERON:0001154	59.13	gold quality
right adrenal gland cortex	UBERON:0035827	55.81	gold quality
islet of Langerhans	UBERON:0000006	53.26	gold quality
left adrenal gland	UBERON:0001234	51.92	gold quality
adrenal gland	UBERON:0002369	51.19	gold quality
left coronary artery	UBERON:0001626	50.91	gold quality
lymph node	UBERON:0000029	49.76	silver quality
left adrenal gland cortex	UBERON:0035825	49.63	gold quality
Brodmann (1909) area 9	UBERON:0013540	49.53	gold quality
blood	UBERON:0000178	49.42	gold quality
right adrenal gland	UBERON:0001233	49.27	gold quality
prefrontal cortex	UBERON:0000451	48.96	silver quality
right coronary artery	UBERON:0001625	48.49	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	47.87	gold quality
urinary bladder	UBERON:0001255	46.18	gold quality
cerebellum	UBERON:0002037	46.16	gold quality
right hemisphere of cerebellum	UBERON:0014890	45.97	gold quality
thoracic aorta	UBERON:0001515	45.62	gold quality
descending thoracic aorta	UBERON:0002345	45.58	gold quality
popliteal artery	UBERON:0002250	45.39	gold quality
ascending aorta	UBERON:0001496	45.33	gold quality
tibial artery	UBERON:0007610	45.28	gold quality
heart	UBERON:0000948	45.26	gold quality
gastrocnemius	UBERON:0001388	44.90	silver quality
cerebellar hemisphere	UBERON:0002245	44.53	gold quality
putamen	UBERON:0001874	44.45	gold quality
heart left ventricle	UBERON:0002084	44.36	silver quality
esophagus mucosa	UBERON:0002469	43.89	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 19)

• This study highlights the importance of lncRNA-MUF as a mediator of mesenchymal stem cell niche modulating hepatocellular carcinoma progression. Furthermore, lncRNA-MUF acted as a competing endogenous RNA for miR-34a, leading to Snail1 upregulation and epithelial-mesenchymal transition activation. (PMID:28947421)
• By performing enrichment analysis based on the co-expression network and regulatory network, authors found that LINC00941 was associated with cancer related biological processes such as cell cycle, cell communication, cell migration, cell division, as well as processes associated with the immune system. (PMID:29653230)
• Elevated expression of LINC00941, which regulates PI3K-AKT signaling and focal adhesion, was negatively associated with lung adenocarcinoma survival. (PMID:30226269)
• lncRNA LINC00941 is a crucial regulator of human epidermal homeostasis. LINC00941 is enriched in progenitor keratinocytes and acts as a repressor of keratinocyte differentiation (PMID:30622217)
• Linc00941 Is a Novel Transforming Growth Factor beta Target That Primes Papillary Thyroid Cancer Metastatic Behavior by Regulating the Expression of Cadherin 6. (PMID:32495722)
• LINC00941 promotes oral squamous cell carcinoma progression via activating CAPRIN2 and canonical WNT/beta-catenin signaling pathway. (PMID:32691935)
• Long noncoding RNA LINC00941 promotes pancreatic cancer progression by competitively binding miR-335-5p to regulate ROCK1-mediated LIMK1/Cofilin-1 signaling. (PMID:33414429)
• LINC00941 promotes proliferation and metastasis of pancreatic adenocarcinoma by competitively binding miR-873-3p and thus upregulates ATXN2. (PMID:33660796)
• Linc00941 regulates esophageal squamous cell carcinoma via functioning as a competing endogenous RNA for miR-877-3p to modulate PMEPA1 expression. (PMID:34254950)
• Expression changes of serum LINC00941 and LINC00514 in HBV infection-related liver diseases and their potential application values. (PMID:34825738)
• Long Noncoding RNA LINC00941 Promotes Cell Proliferation and Invasion by Interacting with hnRNPK in Oral Squamous Cell Carcinoma. (PMID:35037538)
• ATF3 -activated accelerating effect of LINC00941/lncIAPF on fibroblast-to-myofibroblast differentiation by blocking autophagy depending on ELAVL1/HuR in pulmonary fibrosis. (PMID:35427207)
• Long non-coding RNA-LINC00941 promotes the proliferation and invasiveness of glioma cells. (PMID:36375627)
• Reciprocal regulation of LINC00941 and SOX2 promotes progression of esophageal squamous cell carcinoma. (PMID:36717549)
• The human long non-coding RNA LINC00941 and its modes of action in health and disease. (PMID:37418674)
• Knockdown of long non-coding RNA LINC00941 suppressed cell proliferation, colony-formation, and migration of human glioblastoma cell lines. (PMID:37587895)
• LINC00941: a novel player involved in the progression of human cancers. (PMID:37995050)
• lncRNA LINC00941 modulates MTA2/NuRD occupancy to suppress premature human epidermal differentiation. (PMID:38649186)
• Linc00941 fuels ribogenesis and protein synthesis by supporting robust cMYC translation in malignant pleural mesothelioma. (PMID:38729555)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Canonical reviewed UniProt: None (reviewed: )

All UniProt accessions (0):

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 3 (showing top): chr12p11, MEBARKI_HCC_PROGENITOR_FZD8CRD_UP, GSE45365_WT_VS_IFNAR_KO_BCELL_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

3 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000028700 (12:30796324 A>G), RS1000179643 (12:30802484 G>A), RS1000711791 (12:30797311 C>A), RS1001230719 (12:30802882 T>C), RS1002114959 (12:30797915 G>A), RS1002330864 (12:30802585 G>A,C), RS1002572440 (12:30798275 T>G), RS1002773351 (12:30797956 G>A), RS1002933277 (12:30793756 C>G,T), RS1002986882 (12:30793983 G>A), RS1003152668 (12:30799736 C>A,T), RS1003164935 (12:30799753 C>G,T), RS1003521976 (12:30799475 A>G,T), RS1004403765 (12:30797235 T>C), RS1004458577 (12:30798957 T>C)

Disease associations

OMIM: gene MIM:620799 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	decreases expression	2
2-methyl-4-isothiazolin-3-one	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
beta-lapachone	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
fipronil	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
Fulvestrant	decreases methylation	1
Benzo(a)pyrene	increases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Formaldehyde	decreases expression	1
N-Nitrosopyrrolidine	increases expression	1
Aflatoxin B1	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.