LINC01109

Summary

LINC01109 (long intergenic non-protein coding RNA 1109, HGNC:49235) is a long non-coding RNA gene on chromosome 8q21.11.

At a glance

• Clinical variants (ClinVar): 1 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:49235
Approved symbol	LINC01109
Name	long intergenic non-protein coding RNA 1109
Location	8q21.11
Locus type	RNA, long non-coding
Status	Approved
Aliases	lncRNA-N1
Ensembl gene	ENSG00000271167
Entrez	102216341
RNAcentral	URS000212324E — lncRNA, 972 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, 28 present calls, max score 65.78.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2433 / max 13.5777, expressed in 111 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
89433	0.1230	69
205231	0.1203	71

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	65.78	gold quality
ganglionic eminence	UBERON:0004023	58.97	gold quality
cortical plate	UBERON:0005343	57.27	silver quality
prefrontal cortex	UBERON:0000451	53.07	gold quality
heart left ventricle	UBERON:0002084	50.96	silver quality
frontal cortex	UBERON:0001870	48.14	gold quality
primary visual cortex	UBERON:0002436	48.07	silver quality
superior frontal gyrus	UBERON:0002661	47.09	gold quality
blood	UBERON:0000178	46.90	silver quality
cerebral cortex	UBERON:0000956	45.90	gold quality
nucleus accumbens	UBERON:0001882	45.72	gold quality
Brodmann (1909) area 9	UBERON:0013540	45.31	silver quality
brain	UBERON:0000955	44.77	gold quality
cerebellar cortex	UBERON:0002129	44.77	silver quality
cerebellum	UBERON:0002037	44.71	silver quality
cerebellar hemisphere	UBERON:0002245	44.40	silver quality
amygdala	UBERON:0001876	44.05	gold quality
anterior cingulate cortex	UBERON:0009835	44.02	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	43.69	gold quality
right hemisphere of cerebellum	UBERON:0014890	43.41	silver quality
putamen	UBERON:0001874	42.59	silver quality
caudate nucleus	UBERON:0001873	42.50	silver quality
Ammon’s horn	UBERON:0001954	42.22	silver quality
hypothalamus	UBERON:0001898	41.55	gold quality
skin of leg	UBERON:0001511	41.08	silver quality
substantia nigra	UBERON:0002038	40.22	gold quality
right frontal lobe	UBERON:0002810	39.62	silver quality
C1 segment of cervical spinal cord	UBERON:0006469	39.17	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.80

Regulation

Is transcription factor: no

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	1
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): RS1000113910 (8:76403073 G>A,C), RS1000221382 (8:76403400 T>C), RS1000273943 (8:76403107 G>C), RS1001163094 (8:76403185 T>C), RS1001275775 (8:76403379 C>G,T), RS1001556697 (8:76404124 G>A,T), RS1003106424 (8:76405291 A>C), RS1005908110 (8:76402656 C>T), RS1006645394 (8:76402193 C>T), RS1007031520 (8:76403755 G>A), RS1007632755 (8:76402723 A>G), RS1007702396 (8:76403085 A>C,G), RS1008697037 (8:76404857 A>G,T), RS1008744183 (8:76404474 A>C), RS1009042734 (8:76404232 A>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

Clinical trials (associated diseases)

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