LINC00886
gene geneOn this page
Summary
LINC00886 (long intergenic non-protein coding RNA 886, HGNC:48572) is a long non-coding RNA gene on chromosome 3q25.31.
At a glance
- GWAS associations: 7
- Clinical variants (ClinVar): 1 total
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:48572 |
| Approved symbol | LINC00886 |
| Name | long intergenic non-protein coding RNA 886 |
| Location | 3q25.31 |
| Locus type | RNA, long non-coding |
| Status | Approved |
| Ensembl gene | ENSG00000240875 |
| Entrez | 730091 |
| RNAcentral | URS000075C503 — lncRNA, 3354 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 ubiquitous, 169 present calls, max score 93.11.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.6833 / max 40.5320, expressed in 977 samples.
FANTOM5 promoters (4 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 45267 | 2.3827 | 922 |
| 45264 | 0.1969 | 67 |
| 45266 | 0.0797 | 39 |
| 45265 | 0.0240 | 8 |
Top tissues by expression
235 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| kidney epithelium | UBERON:0004819 | 93.11 | gold quality |
| cardiac muscle of right atrium | UBERON:0003379 | 88.13 | gold quality |
| left ventricle myocardium | UBERON:0006566 | 87.89 | gold quality |
| upper arm skin | UBERON:0004263 | 82.76 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 81.11 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 79.97 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 79.67 | gold quality |
| nasal cavity epithelium | UBERON:0005384 | 77.22 | gold quality |
| myocardium | UBERON:0002349 | 76.42 | gold quality |
| skeletal muscle tissue of rectus abdominis | UBERON:0004511 | 76.39 | gold quality |
| cerebellar vermis | UBERON:0004720 | 76.11 | gold quality |
| bronchial epithelial cell | CL:0002328 | 75.65 | gold quality |
| bronchus | UBERON:0002185 | 75.51 | gold quality |
| stromal cell of endometrium | CL:0002255 | 74.40 | gold quality |
| vena cava | UBERON:0004087 | 74.32 | gold quality |
| colonic epithelium | UBERON:0000397 | 74.00 | gold quality |
| right uterine tube | UBERON:0001302 | 73.60 | gold quality |
| body of pancreas | UBERON:0001150 | 73.45 | gold quality |
| bone marrow cell | CL:0002092 | 73.12 | gold quality |
| pancreas | UBERON:0001264 | 72.77 | gold quality |
| cardia of stomach | UBERON:0001162 | 72.73 | gold quality |
| superficial temporal artery | UBERON:0001614 | 72.72 | gold quality |
| quadriceps femoris | UBERON:0001377 | 72.60 | gold quality |
| vastus lateralis | UBERON:0001379 | 72.49 | gold quality |
| pituitary gland | UBERON:0000007 | 72.24 | gold quality |
| layer of synovial tissue | UBERON:0007616 | 72.12 | gold quality |
| superior surface of tongue | UBERON:0007371 | 72.10 | gold quality |
| trachea | UBERON:0003126 | 71.97 | silver quality |
| islet of Langerhans | UBERON:0000006 | 71.91 | gold quality |
| body of tongue | UBERON:0011876 | 71.91 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 0.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 4.52 |
Regulation
Is transcription factor: no
Literature-anchored findings (GeneRIF, showing 3)
- Aberrant DNA hypermethylation-silenced LINC00886 gene accelerates malignant progression of laryngeal carcinoma. (PMID:32111441)
- Downregulation of LINC00886 facilitates epithelial-mesenchymal transition through SIRT7/ELF3/miR-144 pathway in esophageal squamous cell carcinoma. (PMID:35616822)
- LINC00886 Negatively Regulates Malignancy in Anaplastic Thyroid Cancer. (PMID:36726346)
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: 0 (showing top):
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
1 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): RS1000036634 (3:156810185 T>C), RS1000052959 (3:156791096 T>A), RS1000061663 (3:156750734 C>A,G), RS1000104662 (3:156756313 C>T), RS1000165055 (3:156789461 G>A), RS1000256047 (3:156784512 T>C), RS1000345016 (3:156798671 C>A,G), RS1000355568 (3:156777598 T>G), RS1000408100 (3:156778036 A>G,T), RS1000419882 (3:156777988 C>G), RS1000524527 (3:156793223 T>C), RS1000564820 (3:156768721 C>T), RS1000635874 (3:156783474 A>G,T), RS1000732821 (3:156786390 C>T), RS1000745895 (3:156776070 C>T)
Disease associations
OMIM: gene `` | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
7 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST005667_29 | Central corneal thickness | 5.000000e-11 |
| GCST006979_307 | Heel bone mineral density | 5.000000e-20 |
| GCST007656_21 | Chronic obstructive pulmonary disease or resting heart rate (pleiotropy) | 4.000000e-11 |
| GCST009414_12 | Central corneal thickness | 5.000000e-08 |
| GCST010725_61 | Malaria | 1.000000e-06 |
| GCST010725_81 | Malaria | 6.000000e-06 |
| GCST90000654_12 | Central corneal thickness | 9.000000e-15 |
EFO canonical traits (2, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0005213 | central corneal thickness |
| EFO:0009270 | heel bone mineral density |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 0 entries
CTD chemical–gene interactions
15 total (human), top 15 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Nickel | decreases expression | 2 |
| Particulate Matter | affects expression, increases abundance, increases expression | 2 |
| aristolochic acid I | increases expression | 1 |
| 2-amino-9H-pyrido(2,3-b)indole | increases expression | 1 |
| butyraldehyde | decreases expression | 1 |
| pentanal | decreases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| Air Pollutants | affects expression, increases abundance | 1 |
| Benzo(a)pyrene | decreases expression | 1 |
| Dichlorodiphenyl Dichloroethylene | decreases expression | 1 |
| Tobacco Smoke Pollution | increases expression | 1 |
| Propofol | decreases expression | 1 |
| Cyclosporine | increases expression | 1 |
| Cadmium Chloride | decreases expression | 1 |
| Okadaic Acid | decreases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.