LIPE-AS1

Summary

LIPE-AS1 (LIPE antisense RNA 1, HGNC:48589) is a long non-coding RNA gene on chromosome 19q13.2.

At a glance

• Gene type: non-coding (lncRNA) — no protein product.
• Sense gene: antisense to LIPE — the sense gene carries 290 ClinVar variants (the sense gene’s biology, not this transcript’s)
• GTEx eGene: eQTL in 17 tissues, sQTL in 1 (q < 0.05)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:48589
Approved symbol	LIPE-AS1
Name	LIPE antisense RNA 1
Location	19q13.2
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000213904
Ensembl biotype	lncRNA
Entrez	100996307
RNAcentral	URS000075ACDD — lncRNA, 2737 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 127 — 127 lncRNA

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 2, TSL 3: 1, TSL 4: 2, TSL 5: 1

ENST00000457234, ENST00000593491, ENST00000593740, ENST00000594624, ENST00000594688, ENST00000596116, ENST00000597203, ENST00000599276, ENST00000661814, ENST00000685146, ENST00000685574, ENST00000689053, ENST00000701294, ENST00000702399, ENST00000750098, ENST00000750099, ENST00000750100, ENST00000750101, ENST00000750102, ENST00000750103, ENST00000750104, ENST00000750105, ENST00000750106, ENST00000750107, ENST00000750108, ENST00000750109, ENST00000750110, ENST00000750111, ENST00000750112, ENST00000750113, ENST00000750114, ENST00000750115, ENST00000750116, ENST00000750117, ENST00000750118, ENST00000750119, ENST00000750120, ENST00000750121, ENST00000750122, ENST00000750123, ENST00000750124, ENST00000750125, ENST00000750126, ENST00000750127, ENST00000750128, ENST00000750129, ENST00000750130, ENST00000750131, ENST00000750132, ENST00000750133, ENST00000750134, ENST00000750135, ENST00000750136, ENST00000750137, ENST00000750138, ENST00000750139, ENST00000750140, ENST00000750141, ENST00000750142, ENST00000750143, ENST00000750144, ENST00000750145, ENST00000750146, ENST00000750147, ENST00000750148, ENST00000750149, ENST00000750150, ENST00000750151, ENST00000750152, ENST00000750153, ENST00000750154, ENST00000750155, ENST00000750156, ENST00000750157, ENST00000750158, ENST00000750159, ENST00000750160, ENST00000750161, ENST00000750162, ENST00000750163, ENST00000750164, ENST00000750165, ENST00000750166, ENST00000750167, ENST00000750168, ENST00000750169, ENST00000750170, ENST00000750171, ENST00000750172, ENST00000750173, ENST00000750174, ENST00000750175, ENST00000750176, ENST00000750177, ENST00000750178, ENST00000750179, ENST00000750180, ENST00000750181, ENST00000750182, ENST00000750183, ENST00000750184, ENST00000750185, ENST00000750186, ENST00000750187, ENST00000750188, ENST00000750189, ENST00000750190, ENST00000750191, ENST00000750192, ENST00000750193, ENST00000750194, ENST00000750195, ENST00000750196, ENST00000750197, ENST00000750198, ENST00000750199, ENST00000750200, ENST00000750201, ENST00000750202, ENST00000750203, ENST00000750204, ENST00000750205, ENST00000750206, ENST00000750207, ENST00000750208, ENST00000750209, ENST00000750210

RefSeq mRNA: 0

Canonical transcript exons

ENST00000457234 — 5 exons

Exon	Start	End
ENSE00001552276	42485096	42485223
ENSE00001659001	42521992	42522098
ENSE00001681103	42424269	42425204
ENSE00001778910	42510897	42510974
ENSE00001799829	42525618	42525869

Expression profiles

Bgee: expression breadth ubiquitous, 206 present calls, max score 90.16.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.7948 / max 74.1098, expressed in 1747 samples.

Highest expression (Bgee): buccal mucosa cell, monocyte, leukocyte, olfactory segment of nasal mucosa, lower esophagus mucosa.

Genetic regulation across tissues (GTEx eQTL / sQTL)

LIPE-AS1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 17 tissues and its splicing (sQTL) in 1 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

18 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Testis	eqtl	1.2e-10	-0.81	19:42418539:C:T
Esophagus Mucosa	eqtl	2.3e-05	+0.59	19:42395973:A:C
Nerve Tibial	eqtl	4.3e-05	+0.56	19:42192229:G:A
Cells EBV-transformed lymphocytes	eqtl	8.8e-04	-0.41	19:41722521:T:C
Brain Cortex	eqtl	4.2e-03	-0.50	19:42480656:G:GT
Brain Cerebellar Hemisphere	eqtl	5.4e-03	+0.82	19:42395973:A:C
Skin Sun Exposed Lower leg	eqtl	6.0e-03	+0.81	19:42405202:G:A
Brain Cerebellum	eqtl	7.6e-03	-1.31	19:43246785:G:A
Cells Cultured fibroblasts	eqtl	1.3e-02	+0.56	19:43233033:G:C
Heart Left Ventricle	eqtl	1.6e-02	-0.87	19:41797353:T:C
Esophagus Muscularis	eqtl	2.3e-02	+0.32	19:42394603:A:G
Skin Not Sun Exposed Suprapubic	eqtl	2.4e-02	+0.89	19:42404961:C:T
Adrenal Gland	eqtl	3.5e-02	-0.47	19:42490259:C:T
Lung	eqtl	3.9e-02	+0.62	19:42394184:T:G
Artery Aorta	eqtl	4.1e-02	+0.27	19:43033610:A:C
Brain Substantia nigra	eqtl	4.6e-02	-1.66	19:41499484:T:G
Brain Nucleus accumbens basal ganglia	eqtl	4.6e-02	+0.65	19:43043997:G:A
Skin Sun Exposed Lower leg	sqtl	4.6e-02	-0.40	19:42383340:C:T

FANTOM5 promoters

6 alternative TSS:

Promoter ID	TPM avg	Samples expressed
176165	5.5890	1695
176164	2.0814	1135
176168	0.0514	27
176167	0.0323	13
176170	0.0261	7
176169	0.0145	4

Top tissues by expression

showing 100 of 239 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	90.16	gold quality
monocyte	CL:0000576	89.82	gold quality
leukocyte	CL:0000738	89.19	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.79	gold quality
lower esophagus mucosa	UBERON:0035834	87.75	gold quality
tendon of biceps brachii	UBERON:0008188	87.37	gold quality
pancreatic ductal cell	CL:0002079	86.38	silver quality
sural nerve	UBERON:0015488	85.29	gold quality
granulocyte	CL:0000094	85.19	gold quality
hindlimb stylopod muscle	UBERON:0004252	84.90	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.27	gold quality
colonic epithelium	UBERON:0000397	84.14	gold quality
upper arm skin	UBERON:0004263	84.01	gold quality
adenohypophysis	UBERON:0002196	83.65	gold quality
tibialis anterior	UBERON:0001385	83.36	silver quality
deltoid	UBERON:0001476	83.06	silver quality
subcutaneous adipose tissue	UBERON:0002190	82.79	gold quality
omental fat pad	UBERON:0010414	82.77	gold quality
peritoneum	UBERON:0002358	82.76	gold quality
adipose tissue of abdominal region	UBERON:0007808	82.29	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.05	gold quality
pituitary gland	UBERON:0000007	81.93	gold quality
kidney epithelium	UBERON:0004819	81.78	gold quality
cardiac muscle of right atrium	UBERON:0003379	81.30	gold quality
left ventricle myocardium	UBERON:0006566	81.30	gold quality
tendon	UBERON:0000043	81.17	gold quality
mucosa of transverse colon	UBERON:0004991	81.09	gold quality
cerebellar vermis	UBERON:0004720	80.82	gold quality
left adrenal gland cortex	UBERON:0035825	80.52	gold quality
adipose tissue	UBERON:0001013	80.00	gold quality
calcaneal tendon	UBERON:0003701	79.87	gold quality
adrenal cortex	UBERON:0001235	79.78	gold quality
prefrontal cortex	UBERON:0000451	79.60	gold quality
pericardium	UBERON:0002407	79.56	gold quality
nasal cavity epithelium	UBERON:0005384	79.34	gold quality
hypothalamus	UBERON:0001898	79.14	gold quality
left testis	UBERON:0004533	79.11	gold quality
left adrenal gland	UBERON:0001234	79.07	gold quality
putamen	UBERON:0001874	79.02	gold quality
quadriceps femoris	UBERON:0001377	78.98	gold quality
nasal cavity mucosa	UBERON:0001826	78.98	gold quality
esophagus mucosa	UBERON:0002469	78.92	gold quality
adrenal gland	UBERON:0002369	78.85	gold quality
right testis	UBERON:0004534	78.71	gold quality
right adrenal gland	UBERON:0001233	78.70	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	78.70	gold quality
vena cava	UBERON:0004087	78.59	silver quality
testis	UBERON:0000473	78.57	gold quality
skeletal muscle tissue	UBERON:0001134	78.56	gold quality
bone marrow	UBERON:0002371	78.46	gold quality
adrenal tissue	UBERON:0018303	78.44	gold quality
nipple	UBERON:0002030	78.37	silver quality
esophagus	UBERON:0001043	78.33	gold quality
nucleus accumbens	UBERON:0001882	78.10	gold quality
amygdala	UBERON:0001876	78.04	gold quality
muscle tissue	UBERON:0002385	78.02	gold quality
right adrenal gland cortex	UBERON:0035827	78.02	gold quality
body of tongue	UBERON:0011876	78.00	gold quality
prostate gland	UBERON:0002367	77.89	gold quality
uterine cervix	UBERON:0000002	77.82	gold quality
lower esophagus	UBERON:0013473	77.77	gold quality
vastus lateralis	UBERON:0001379	77.76	gold quality
lower esophagus muscularis layer	UBERON:0035833	77.76	gold quality
Brodmann (1909) area 9	UBERON:0013540	77.67	gold quality
tibial nerve	UBERON:0001323	77.58	gold quality
cortex of kidney	UBERON:0001225	77.52	gold quality
lateral globus pallidus	UBERON:0002476	77.34	silver quality
esophagogastric junction muscularis propria	UBERON:0035841	77.17	gold quality
substantia nigra	UBERON:0002038	76.86	gold quality
saliva-secreting gland	UBERON:0001044	76.81	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	76.77	gold quality
ectocervix	UBERON:0012249	76.76	gold quality
globus pallidus	UBERON:0001875	76.72	gold quality
blood	UBERON:0000178	76.70	gold quality
minor salivary gland	UBERON:0001830	76.66	gold quality
midbrain	UBERON:0001891	76.66	gold quality
anterior cingulate cortex	UBERON:0009835	76.65	gold quality
medial globus pallidus	UBERON:0002477	76.61	gold quality
forebrain	UBERON:0001890	76.55	gold quality
spinal cord	UBERON:0002240	76.52	gold quality
muscle layer of sigmoid colon	UBERON:0035805	76.48	gold quality
frontal cortex	UBERON:0001870	76.46	gold quality
caudate nucleus	UBERON:0001873	76.43	gold quality
left lobe of thyroid gland	UBERON:0001120	76.40	gold quality
stromal cell of endometrium	CL:0002255	76.36	gold quality
spleen	UBERON:0002106	76.31	gold quality
neocortex	UBERON:0001950	76.25	gold quality
brain	UBERON:0000955	76.19	gold quality
vagina	UBERON:0000996	76.12	gold quality
primary visual cortex	UBERON:0002436	76.08	gold quality
endocervix	UBERON:0000458	75.92	gold quality
trachea	UBERON:0003126	75.91	silver quality
thyroid gland	UBERON:0002046	75.84	gold quality
pylorus	UBERON:0001166	75.79	silver quality
epithelial cell of pancreas	CL:0000083	75.75	gold quality
occipital lobe	UBERON:0002021	75.75	gold quality
temporal lobe	UBERON:0001871	75.71	gold quality
right lobe of thyroid gland	UBERON:0001119	75.57	gold quality
mouth mucosa	UBERON:0003729	75.56	gold quality
fundus of stomach	UBERON:0001160	75.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.66

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Follicular fluid-derived exosomal LncRNA LIPE-AS1 modulates steroid metabolism and survival of granulosa cells leading to oocyte maturation arrest in polycystic ovary syndrome. (PMID:38656738)

Cross-species orthologs

0 orthologs

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
PSG8	protein-coding	440533
PSG3	protein-coding	5671
MIR8077	ncRNA	102465875
MEGF8	protein-coding	1954
CXCL17	protein-coding	284340
LIPE	protein-coding	3991
CNFN	protein-coding	84518
PRR19	protein-coding	284338
TMEM145	protein-coding	284339
PAFAH1B3	protein-coding	5050
CEACAM8	protein-coding	1088
CEACAM1	protein-coding	634

Protein

Non-coding RNA — no protein product.

Function

Gene-set membership (MSigDB)

This non-coding RNA is a member of 28 curated MSigDB gene sets — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data).

ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, CREB3L4_TARGET_GENES, E2F2_TARGET_GENES, ELF2_TARGET_GENES, FEV_TARGET_GENES, PRKDC_TARGET_GENES, SNIP1_TARGET_GENES, TEAD2_TARGET_GENES, ZBTB12_TARGET_GENES, ZFHX3_TARGET_GENES, ZIM3_TARGET_GENES, ZNF33A_TARGET_GENES, ZNF350_TARGET_GENES, ZNF436_TARGET_GENES, DESCARTES_MAIN_FETAL_SLC26A4_PAEP_POSITIVE_CELLS, SETD1A_TARGET_GENES, BRCA2_TARGET_GENES, NKX2_5_TARGET_GENES, AEBP2_TARGET_GENES, ZZZ3_TARGET_GENES, MYOCD_TARGET_GENES, SUPT20H_TARGET_GENES, TET1_TARGET_GENES, WRNIP1_TARGET_GENES, BARX2_TARGET_GENES, HE_LIM_SUN_FETAL_LUNG_C1_SMG_CELL, chr19q13

ncRNA interactions

Experimentally supported non-coding-RNA interaction partners (NPInter).

showing 60 of 174 interaction partners:

Partner	Partner type	Level	Source
ADAR	protein	RNA-Protein	High-throughput data
WDR33	protein	RNA-Protein	High-throughput data
HNRH1	protein	RNA-Protein	High-throughput data combine LncPro prediction
HNRNPA1	protein	RNA-Protein	GSE83923;ENCODE;High-throughput data
hnRNPM	protein	RNA-Protein	ENCODE;High-throughput data
CPSF6	protein	RNA-Protein	High-throughput data combine LncPro prediction
FXR2	protein	RNA-Protein	High-throughput data combine LncPro prediction
FXR1	protein	RNA-Protein	High-throughput data
LIN28A	protein	RNA-Protein	High-throughput data
TARDBP	protein	RNA-Protein	ENCODE;High-throughput data
TDP-43	protein	RNA-Protein	High-throughput data
RBM6	protein	RNA-Protein	High-throughput data
RBM10	protein	RNA-Protein	High-throughput data
MOV10	protein	RNA-Protein	High-throughput data;GSE70061
UPF1	protein	RNA-Protein	High-throughput data
hnRNPA2B1	protein	RNA-Protein	High-throughput data
FUS	protein	RNA-Protein	High-throughput data combine LncPro prediction
hsa-mir-21-3p	miRNA	RNA-RNA	miRanda with Ago CLIP data
hsa-mir-223-3p	miRNA	RNA-RNA	miRanda with Ago CLIP data
hsa-miR-22-3p	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-mir-28-3p	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-miR-3139	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-miR-370	miRNA	RNA-RNA	miRanda with Ago CLIP data
hsa-miR-4644	miRNA	RNA-RNA	miRanda with Ago CLIP data
hsa-miR-668-3p	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-miR-708-3p	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-mir-128	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-miR-144-3p	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-miR-199a-5p	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-miR-199b-5p	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-mir-216a-3p	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-miR-3129-5p	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-miR-3681-3p	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-miR-382-5p	miRNA	RNA-RNA	TargetScan with Ago CLIP data
hsa-miR-433	miRNA	RNA-RNA	TargetScan with Ago CLIP data
BCCIP	protein	RNA-Protein	ENCODE
BUD13	protein	RNA-Protein	ENCODE
CSTF2	protein	RNA-Protein	ENCODE
CSTF2T	protein	RNA-Protein	ENCODE
DDX3X	protein	RNA-Protein	ENCODE
DDX55	protein	RNA-Protein	ENCODE
DDX59	protein	RNA-Protein	ENCODE
DDX6	protein	RNA-Protein	ENCODE
DGCR8	protein	RNA-Protein	ENCODE
DHX30	protein	RNA-Protein	ENCODE
DKC1	protein	RNA-Protein	ENCODE
EIF3D	protein	RNA-Protein	ENCODE
EIF3H	protein	RNA-Protein	ENCODE
FAM120A	protein	RNA-Protein	ENCODE
FAKD2	protein	RNA-Protein	ENCODE
FKBP4	protein	RNA-Protein	ENCODE
FUBP3	protein	RNA-Protein	ENCODE
GRWD1	protein	RNA-Protein	ENCODE
HNRNPUL1	protein	RNA-Protein	ENCODE
hnRNPC	protein	RNA-Protein	ENCODE
HNRPK	protein	RNA-Protein	ENCODE
hnRNPL	protein	RNA-Protein	ENCODE
HNRNPU	protein	RNA-Protein	ENCODE
IF2B1	protein	RNA-Protein	ENCODE;GSE78507
IGF2BP3	protein	RNA-Protein	ENCODE;GSE78507

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

ncRNA–drug associations

Curated non-coding-RNA → drug associations (drug response / resistance / target).

showing 1 of 2 ncRNA–drug associations:

Drug	Relation	Effect	Condition
Cisplatin	drug_resistance	resistant	cell line (FaDu)