LINC01249

Summary

LINC01249 (long intergenic non-protein coding RNA 1249, HGNC:49843) is a long non-coding RNA gene on chromosome 2p25.2.

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:49843
Approved symbol	LINC01249
Name	long intergenic non-protein coding RNA 1249
Location	2p25.2
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000231532
Ensembl biotype	lncRNA
Entrez	727982
RNAcentral	URS000075A47C — lncRNA, 2674 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 lncRNA

ENST00000412134, ENST00000421212, ENST00000432314, ENST00000659398, ENST00000823876

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000412134 — 5 exons

Exon	Start	End
ENSE00001607955	4634894	4635059
ENSE00001610065	4651313	4651529
ENSE00001612391	4652513	4652573
ENSE00001764618	4628216	4630390
ENSE00003856396	4656166	4656498

Expression profiles

Bgee: expression breadth broad, 90 present calls, max score 80.60.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0171 / max 14.8858, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
26728	0.0122	3
26727	0.0050	3

Top tissues by expression

90 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	80.60	gold quality
bone marrow cell	CL:0002092	78.27	gold quality
right testis	UBERON:0004534	68.61	gold quality
testis	UBERON:0000473	67.55	gold quality
urinary bladder	UBERON:0001255	67.07	silver quality
liver	UBERON:0002107	66.63	gold quality
left testis	UBERON:0004533	65.95	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	65.17	gold quality
tonsil	UBERON:0002372	61.14	gold quality
ganglionic eminence	UBERON:0004023	57.24	silver quality
monocyte	CL:0000576	57.12	gold quality
cortex of kidney	UBERON:0001225	56.53	gold quality
cortical plate	UBERON:0005343	55.16	silver quality
small intestine	UBERON:0002108	54.92	gold quality
placenta	UBERON:0001987	53.65	gold quality
blood	UBERON:0000178	51.41	silver quality
pancreas	UBERON:0001264	50.97	gold quality
islet of Langerhans	UBERON:0000006	49.16	gold quality
kidney	UBERON:0002113	48.87	gold quality
superior frontal gyrus	UBERON:0002661	48.59	gold quality
multicellular organism	UBERON:0000468	48.39	gold quality
muscle of leg	UBERON:0001383	47.08	gold quality
gastrocnemius	UBERON:0001388	46.70	gold quality
adrenal gland	UBERON:0002369	46.11	silver quality
stomach	UBERON:0000945	46.01	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	45.88	silver quality
saliva-secreting gland	UBERON:0001044	45.58	gold quality
prefrontal cortex	UBERON:0000451	45.54	silver quality
gall bladder	UBERON:0002110	44.41	silver quality
colon	UBERON:0001155	44.18	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.08

Regulation

Is transcription factor: no

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.