LINC01016

Summary

LINC01016 (long intergenic non-protein coding RNA 1016, HGNC:48991) is a long non-coding RNA gene on chromosome 6p21.31.

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:48991
Approved symbol	LINC01016
Name	long intergenic non-protein coding RNA 1016
Location	6p21.31
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000249346
Ensembl biotype	lncRNA
Entrez	100507584
RNAcentral	URS0000759DB1 — lncRNA, 3165 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 34 lncRNA

ENST00000506222, ENST00000525746, ENST00000525912, ENST00000531046, ENST00000533304, ENST00000655885, ENST00000656180, ENST00000656906, ENST00000659818, ENST00000661137, ENST00000666060, ENST00000671143, ENST00000799599, ENST00000799600, ENST00000799601, ENST00000799602, ENST00000799603, ENST00000799604, ENST00000799605, ENST00000799606, ENST00000799607, ENST00000799608, ENST00000799609, ENST00000799610, ENST00000799611, ENST00000799612, ENST00000799613, ENST00000799614, ENST00000799615, ENST00000799616, ENST00000799617, ENST00000799618, ENST00000799619, ENST00000799620

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000506222 — 3 exons

Exon	Start	End
ENSE00004188292	33889511	33892451
ENSE00004188305	33893579	33893699
ENSE00004188311	33896819	33897033

Expression profiles

Bgee: expression breadth ubiquitous, 135 present calls, max score 96.61.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4223 / max 226.4447, expressed in 97 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
73197	0.2029	93
73194	0.1642	3
73193	0.0508	3
73196	0.0044	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	96.61	gold quality
right testis	UBERON:0004534	96.26	gold quality
testis	UBERON:0000473	93.44	gold quality
sperm	CL:0000019	88.83	gold quality
adult organism	UBERON:0007023	88.18	gold quality
colonic epithelium	UBERON:0000397	83.12	gold quality
lower lobe of lung	UBERON:0008949	82.81	silver quality
mammary duct	UBERON:0001765	82.45	gold quality
epithelium of nasopharynx	UBERON:0001951	81.78	gold quality
germinal epithelium of ovary	UBERON:0001304	77.10	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.89	gold quality
gingival epithelium	UBERON:0001949	74.42	gold quality
mucosa of paranasal sinus	UBERON:0005030	73.25	gold quality
endocervix	UBERON:0000458	72.27	gold quality
smooth muscle tissue	UBERON:0001135	72.25	gold quality
body of uterus	UBERON:0009853	71.52	gold quality
ectocervix	UBERON:0012249	70.17	gold quality
uterine cervix	UBERON:0000002	69.91	gold quality
gingiva	UBERON:0001828	68.66	gold quality
cerebellar vermis	UBERON:0004720	68.39	gold quality
superficial temporal artery	UBERON:0001614	67.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	67.47	gold quality
visceral pleura	UBERON:0002401	67.31	gold quality
parietal pleura	UBERON:0002400	67.29	gold quality
mammary gland	UBERON:0001911	66.93	gold quality
amniotic fluid	UBERON:0000173	66.59	gold quality
thoracic mammary gland	UBERON:0005200	66.41	gold quality
uterus	UBERON:0000995	65.26	gold quality
upper leg skin	UBERON:0004262	65.16	gold quality
myometrium	UBERON:0001296	65.13	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.11

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• ETS-1-activated LINC01016 over-expression promotes tumor progression via suppression of RFFL-mediated DHX9 ubiquitination degradation in breast cancers. (PMID:37550275)

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.