LINC00299

Summary

LINC00299 (long intergenic non-protein coding RNA 299, HGNC:27940) is a long non-coding RNA gene on chromosome 2p25.1.

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:27940
Approved symbol	LINC00299
Name	long intergenic non-protein coding RNA 299
Location	2p25.1
Locus type	RNA, long non-coding
Status	Approved
Aliases	FLJ45673
Ensembl gene	ENSG00000236790
Ensembl biotype	lncRNA
Entrez	339789
RNAcentral	URS000075F09A — lncRNA, 2000 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 120 — 120 lncRNA

ENST00000418358, ENST00000426969, ENST00000430192, ENST00000436187, ENST00000442956, ENST00000444688, ENST00000454043, ENST00000454224, ENST00000456681, ENST00000648035, ENST00000648900, ENST00000650238, ENST00000654099, ENST00000655006, ENST00000655346, ENST00000655671, ENST00000657091, ENST00000657310, ENST00000658862, ENST00000660229, ENST00000661371, ENST00000662336, ENST00000662379, ENST00000663636, ENST00000664004, ENST00000664226, ENST00000664719, ENST00000664728, ENST00000665772, ENST00000666457, ENST00000667380, ENST00000668369, ENST00000668575, ENST00000669954, ENST00000670008, ENST00000670389, ENST00000685270, ENST00000685893, ENST00000686209, ENST00000689905, ENST00000691773, ENST00000691916, ENST00000692033, ENST00000701314, ENST00000702154, ENST00000702808, ENST00000715733, ENST00000715734, ENST00000761481, ENST00000761482, ENST00000761483, ENST00000761484, ENST00000761485, ENST00000764355, ENST00000764356, ENST00000764357, ENST00000764358, ENST00000764359, ENST00000764360, ENST00000764361, ENST00000764362, ENST00000764363, ENST00000764364, ENST00000764365, ENST00000764366, ENST00000764367, ENST00000764368, ENST00000764369, ENST00000764370, ENST00000764371, ENST00000764372, ENST00000764373, ENST00000764374, ENST00000764375, ENST00000764376, ENST00000764377, ENST00000764378, ENST00000764379, ENST00000764380, ENST00000764381, ENST00000764382, ENST00000764383, ENST00000764384, ENST00000764385, ENST00000764386, ENST00000764387, ENST00000764388, ENST00000764389, ENST00000764390, ENST00000764391, ENST00000764392, ENST00000764393, ENST00000764394, ENST00000764395, ENST00000764396, ENST00000764397, ENST00000764398, ENST00000764399, ENST00000764400, ENST00000764401, ENST00000764402, ENST00000764403, ENST00000764404, ENST00000764405, ENST00000764406, ENST00000764407, ENST00000764408, ENST00000764409, ENST00000764410, ENST00000779383, ENST00000779384, ENST00000779385, ENST00000779386, ENST00000779387, ENST00000779388, ENST00000779389, ENST00000779390, ENST00000779391, ENST00000779392, ENST00000779393

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000418358 — 3 exons

Exon	Start	End
ENSE00001651922	8575366	8575501
ENSE00001747153	8545148	8545236
ENSE00004121332	8543556	8544402

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 84.50.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5426 / max 43.0608, expressed in 211 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter ID	TPM avg	Samples expressed
26780	0.6415	107
26779	0.2855	134
26790	0.2837	105
26788	0.1069	51
26778	0.0898	28
26776	0.0733	42
26786	0.0644	29
26777	0.0483	38
26789	0.0445	17
26785	0.0430	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	84.50	gold quality
bone marrow cell	CL:0002092	79.46	gold quality
adrenal tissue	UBERON:0018303	79.25	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.24	gold quality
right lobe of liver	UBERON:0001114	76.33	gold quality
left adrenal gland cortex	UBERON:0035825	74.71	gold quality
right frontal lobe	UBERON:0002810	73.98	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.95	gold quality
right adrenal gland	UBERON:0001233	73.65	gold quality
right adrenal gland cortex	UBERON:0035827	73.55	gold quality
Brodmann (1909) area 9	UBERON:0013540	73.52	gold quality
amygdala	UBERON:0001876	73.42	gold quality
left adrenal gland	UBERON:0001234	73.41	gold quality
anterior cingulate cortex	UBERON:0009835	73.34	gold quality
caudate nucleus	UBERON:0001873	72.90	gold quality
putamen	UBERON:0001874	72.68	gold quality
colonic epithelium	UBERON:0000397	72.63	gold quality
adrenal gland	UBERON:0002369	72.37	gold quality
adrenal cortex	UBERON:0001235	72.09	gold quality
nucleus accumbens	UBERON:0001882	71.31	gold quality
gall bladder	UBERON:0002110	69.13	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	68.66	gold quality
leukocyte	CL:0000738	68.30	gold quality
monocyte	CL:0000576	67.35	gold quality
corpus callosum	UBERON:0002336	67.25	gold quality
prefrontal cortex	UBERON:0000451	66.35	gold quality
blood	UBERON:0000178	66.25	gold quality
spleen	UBERON:0002106	65.87	gold quality
neocortex	UBERON:0001950	65.66	gold quality
vermiform appendix	UBERON:0001154	65.53	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	94.12
E-HCAD-25	yes	24.51
E-ANND-3	yes	6.64

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 4)

• Disruption of LINC00299 in subjects with neurodevelopmental disabilities implicate this particular noncoding RNA in brain development and raise the possibility that, as a class, abnormalities of lincRNAs may play a significant role in human developmental disorders. (PMID:23217328)
• Hypermethylation of LINC00299 in peripheral blood may constitute a useful circulating biomarker for TNBC. (PMID:30208740)
• Expressions of Linc00299 and miR-490-3p were upregulated and downregulated in atherosclerosis patients, respectively. (PMID:30734057)
• Long non-coding RNA LINC00299 knockdown inhibits ox-LDL-induced T/G HA-VSMC injury by regulating miR-135a-5p/XBP1 axis in atherosclerosis. (PMID:32700888)

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.