LINC02399

Summary

LINC02399 (long intergenic non-protein coding RNA 2399, HGNC:53326) is a long non-coding RNA gene on chromosome 12q21.33.

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53326
Approved symbol	LINC02399
Name	long intergenic non-protein coding RNA 2399
Location	12q21.33
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000257725
Entrez	105369891
RNAcentral	URS0000A775BE — lncRNA, 413 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, 57 present calls, max score 76.11.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.11	gold quality
bone marrow cell	CL:0002092	71.23	silver quality
bone marrow	UBERON:0002371	67.74	gold quality
left testis	UBERON:0004533	62.25	gold quality
right testis	UBERON:0004534	61.96	gold quality
testis	UBERON:0000473	61.57	gold quality
lymph node	UBERON:0000029	60.47	gold quality
lung	UBERON:0002048	57.10	gold quality
islet of Langerhans	UBERON:0000006	56.90	gold quality
calcaneal tendon	UBERON:0003701	56.44	gold quality
vermiform appendix	UBERON:0001154	55.96	gold quality
monocyte	CL:0000576	54.81	gold quality
gastrocnemius	UBERON:0001388	53.95	gold quality
multicellular organism	UBERON:0000468	53.77	gold quality
blood	UBERON:0000178	52.01	gold quality
rectum	UBERON:0001052	51.95	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	51.40	gold quality
smooth muscle tissue	UBERON:0001135	50.83	gold quality
thoracic mammary gland	UBERON:0005200	50.79	gold quality
heart	UBERON:0000948	50.64	gold quality
heart left ventricle	UBERON:0002084	49.55	gold quality
tibial artery	UBERON:0007610	49.36	silver quality
right atrium auricular region	UBERON:0006631	47.70	gold quality
tonsil	UBERON:0002372	47.66	gold quality
Brodmann (1909) area 9	UBERON:0013540	47.60	silver quality
body of pancreas	UBERON:0001150	47.33	gold quality
colon	UBERON:0001155	46.85	gold quality
lower esophagus muscularis layer	UBERON:0035833	46.79	gold quality
body of stomach	UBERON:0001161	46.74	gold quality
stomach	UBERON:0000945	46.73	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.72

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

0 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): RS1000454170 (12:89946873 T>G), RS1000511244 (12:89947220 G>A), RS1000565432 (12:89946957 G>A,T), RS1000737566 (12:89945801 C>T), RS1000805480 (12:89947091 G>C), RS1001087986 (12:89946164 G>A), RS1001340941 (12:89946509 T>A), RS1002900831 (12:89949580 A>G), RS1003058783 (12:89947518 A>G), RS1003278677 (12:89949865 A>G), RS1003344760 (12:89949794 A>T), RS1003417612 (12:89947906 C>T), RS1003806525 (12:89949471 A>G,T), RS1004740736 (12:89946842 T>C), RS1004794876 (12:89946554 T>C)

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Smoke	increases expression	1

Clinical trials (associated diseases)

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