EPCIP-AS1

Summary

EPCIP-AS1 (EPCIP antisense RNA 1, HGNC:1290) is a long non-coding RNA gene on chromosome 21q22.11.

At a glance

• Gene type: non-coding (lncRNA) — no protein product.
• Sense gene: antisense to EPCIP — the sense gene carries 1 GWAS associations, 13 ClinVar variants (the sense gene’s biology, not this transcript’s)
• GTEx eGene: eQTL in 43 tissues, sQTL in 6 (q < 0.05)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1290
Approved symbol	EPCIP-AS1
Name	EPCIP antisense RNA 1
Location	21q22.11
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000205930
Ensembl biotype	lncRNA
Entrez	54067
RNAcentral	URS000075B613 — lncRNA, 1215 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 39 — 39 lncRNA

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

ENST00000382375, ENST00000382377, ENST00000382378, ENST00000454365, ENST00000477513, ENST00000491756, ENST00000612326, ENST00000650763, ENST00000655231, ENST00000661254, ENST00000663888, ENST00000666106, ENST00000669746, ENST00000700822, ENST00000701283, ENST00000701622, ENST00000777210, ENST00000777211, ENST00000777212, ENST00000777213, ENST00000777214, ENST00000777215, ENST00000777216, ENST00000777217, ENST00000777218, ENST00000777219, ENST00000777220, ENST00000777221, ENST00000777222, ENST00000777223, ENST00000777224, ENST00000777225, ENST00000777226, ENST00000777227, ENST00000777228, ENST00000777229, ENST00000777230, ENST00000777231, ENST00000777232

RefSeq mRNA: 0

Canonical transcript exons

ENST00000382375 — 4 exons

Exon	Start	End
ENSE00001816474	32796939	32798969
ENSE00002479956	32784797	32784919
ENSE00002534803	32772100	32772308
ENSE00003735243	32788612	32788701

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 78.45.

FANTOM5 (CAGE): breadth broad, TPM avg 2.1636 / max 49.4434, expressed in 855 samples.

Highest expression (Bgee): sural nerve, male germ line stem cell (sensu Vertebrata) in testis, corpus callosum, calcaneal tendon, testis.

Genetic regulation across tissues (GTEx eQTL / sQTL)

EPCIP-AS1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 43 tissues and its splicing (sQTL) in 6 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 49 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Skin Sun Exposed Lower leg	eqtl	9.0e-43	+0.46	21:32772234:A:G
Adipose Subcutaneous	eqtl	6.4e-41	+0.50	21:32772234:A:G
Thyroid	eqtl	1.3e-38	+0.47	21:32772234:A:G
Esophagus Muscularis	eqtl	8.2e-34	+0.52	21:32772234:A:G
Artery Tibial	eqtl	1.2e-30	+0.42	21:32772234:A:G
Skin Not Sun Exposed Suprapubic	eqtl	1.3e-27	+0.39	21:32772234:A:G
Pituitary	eqtl	1.5e-27	+1.07	21:32790692:T:C
Testis	sqtl	1.8e-27	-0.74	21:32885406:A:C
Esophagus Mucosa	eqtl	3.0e-26	+0.40	21:32772234:A:G
Brain Cerebellar Hemisphere	eqtl	3.3e-21	+0.62	21:32773868:C:G
Esophagus Gastroesophageal Junction	eqtl	6.0e-21	+0.49	21:32772234:A:G
Breast Mammary Tissue	eqtl	7.7e-21	+0.32	21:32772234:A:G
Nerve Tibial	eqtl	1.2e-19	+0.26	21:32772234:A:G
Colon Transverse	eqtl	5.4e-19	+0.38	21:32772234:A:G
Muscle Skeletal	eqtl	4.8e-18	+0.34	21:32772234:A:G
Lung	eqtl	1.6e-17	+0.31	21:32772234:A:G
Cells Cultured fibroblasts	eqtl	2.6e-17	-0.39	21:32725674:G:A
Spleen	eqtl	3.1e-16	+0.52	21:32772234:A:G
Brain Cerebellum	eqtl	4.4e-16	+0.61	21:32773868:C:G
Adipose Visceral Omentum	eqtl	5.9e-16	+0.33	21:32775534:A:G

FANTOM5 promoters

1 alternative TSS:

Promoter ID	TPM avg	Samples expressed
188829	2.1636	855

Top tissues by expression

showing 100 of 136 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	78.45	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.55	gold quality
corpus callosum	UBERON:0002336	75.90	gold quality
calcaneal tendon	UBERON:0003701	73.65	gold quality
right testis	UBERON:0004534	73.34	gold quality
islet of Langerhans	UBERON:0000006	73.25	gold quality
adrenal tissue	UBERON:0018303	72.96	gold quality
testis	UBERON:0000473	72.86	gold quality
left testis	UBERON:0004533	72.86	gold quality
colonic epithelium	UBERON:0000397	72.72	gold quality
bone marrow cell	CL:0002092	72.24	silver quality
ovary	UBERON:0000992	72.11	gold quality
left ovary	UBERON:0002119	71.72	gold quality
right ovary	UBERON:0002118	70.64	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	70.59	gold quality
spinal cord	UBERON:0002240	70.54	gold quality
right uterine tube	UBERON:0001302	70.26	gold quality
urinary bladder	UBERON:0001255	70.21	gold quality
lymph node	UBERON:0000029	69.33	gold quality
tonsil	UBERON:0002372	69.02	gold quality
monocyte	CL:0000576	68.60	gold quality
leukocyte	CL:0000738	68.50	gold quality
substantia nigra	UBERON:0002038	68.45	gold quality
pancreas	UBERON:0001264	68.04	gold quality
stromal cell of endometrium	CL:0002255	67.16	gold quality
ventricular zone	UBERON:0003053	66.89	gold quality
muscle tissue	UBERON:0002385	66.74	gold quality
kidney	UBERON:0002113	66.70	gold quality
skeletal muscle tissue	UBERON:0001134	66.65	gold quality
cortex of kidney	UBERON:0001225	66.49	gold quality
endocervix	UBERON:0000458	66.47	gold quality
thymus	UBERON:0002370	66.44	gold quality
smooth muscle tissue	UBERON:0001135	66.25	gold quality
thyroid gland	UBERON:0002046	66.22	gold quality
tibial nerve	UBERON:0001323	66.19	gold quality
adrenal gland	UBERON:0002369	66.13	gold quality
fallopian tube	UBERON:0003889	66.04	gold quality
uterine cervix	UBERON:0000002	65.91	gold quality
ganglionic eminence	UBERON:0004023	65.88	gold quality
amygdala	UBERON:0001876	65.75	gold quality
right adrenal gland	UBERON:0001233	65.74	gold quality
popliteal artery	UBERON:0002250	65.70	gold quality
tibial artery	UBERON:0007610	65.66	gold quality
right lobe of thyroid gland	UBERON:0001119	65.64	gold quality
left lobe of thyroid gland	UBERON:0001120	65.58	gold quality
muscle layer of sigmoid colon	UBERON:0035805	65.30	gold quality
body of pancreas	UBERON:0001150	65.19	gold quality
left adrenal gland	UBERON:0001234	65.18	gold quality
myometrium	UBERON:0001296	65.18	gold quality
Ammon’s horn	UBERON:0001954	65.13	gold quality
bone marrow	UBERON:0002371	65.12	silver quality
left adrenal gland cortex	UBERON:0035825	65.12	gold quality
lower esophagus muscularis layer	UBERON:0035833	65.09	gold quality
lower esophagus	UBERON:0013473	65.08	gold quality
pituitary gland	UBERON:0000007	65.06	gold quality
adult mammalian kidney	UBERON:0000082	65.05	gold quality
body of uterus	UBERON:0009853	65.04	gold quality
fundus of stomach	UBERON:0001160	64.97	gold quality
rectum	UBERON:0001052	64.81	gold quality
endometrium	UBERON:0001295	64.81	gold quality
right adrenal gland cortex	UBERON:0035827	64.80	gold quality
thoracic mammary gland	UBERON:0005200	64.77	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	64.55	gold quality
spleen	UBERON:0002106	64.51	gold quality
hypothalamus	UBERON:0001898	64.38	gold quality
putamen	UBERON:0001874	64.35	gold quality
metanephros cortex	UBERON:0010533	64.33	gold quality
primary visual cortex	UBERON:0002436	64.31	gold quality
descending thoracic aorta	UBERON:0002345	64.30	gold quality
colon	UBERON:0001155	64.24	gold quality
right atrium auricular region	UBERON:0006631	64.12	gold quality
multicellular organism	UBERON:0000468	64.02	gold quality
apex of heart	UBERON:0002098	64.02	gold quality
right coronary artery	UBERON:0001625	63.99	gold quality
intestine	UBERON:0000160	63.96	gold quality
adenohypophysis	UBERON:0002196	63.85	gold quality
superior frontal gyrus	UBERON:0002661	63.83	gold quality
saliva-secreting gland	UBERON:0001044	63.71	gold quality
heart	UBERON:0000948	63.59	gold quality
brain	UBERON:0000955	63.53	gold quality
blood	UBERON:0000178	63.50	gold quality
minor salivary gland	UBERON:0001830	63.47	gold quality
thoracic aorta	UBERON:0001515	63.45	gold quality
cortical plate	UBERON:0005343	63.37	gold quality
ectocervix	UBERON:0012249	63.37	gold quality
ascending aorta	UBERON:0001496	63.35	gold quality
liver	UBERON:0002107	63.35	gold quality
hindlimb stylopod muscle	UBERON:0004252	63.29	gold quality
small intestine	UBERON:0002108	63.26	gold quality
gall bladder	UBERON:0002110	63.26	gold quality
vermiform appendix	UBERON:0001154	63.23	gold quality
caudate nucleus	UBERON:0001873	63.20	gold quality
prostate gland	UBERON:0002367	63.15	gold quality
left coronary artery	UBERON:0001626	63.07	gold quality
heart left ventricle	UBERON:0002084	63.06	gold quality
vagina	UBERON:0000996	62.94	gold quality
granulocyte	CL:0000094	62.90	gold quality
left uterine tube	UBERON:0001303	62.89	gold quality
transverse colon	UBERON:0001157	62.79	gold quality
cerebellum	UBERON:0002037	62.71	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.40

Regulation

Is transcription factor: no

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
EPCIP	protein-coding	56245
SYNJ1	protein-coding	8867
PAXBP1	protein-coding	94104
LINC01690	ncRNA	102724502
PAXBP1-AS1	ncRNA	100506215
CFAP298-TCP10L	protein-coding	110091775
CFAP298	protein-coding	56683

Protein

Non-coding RNA — no protein product.

Function

Gene-set membership (MSigDB)

This non-coding RNA is a member of 84 curated MSigDB gene sets — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data).

chr21q22, ARID5B_TARGET_GENES, BANP_TARGET_GENES, CENPT_TARGET_GENES, CHAMP1_TARGET_GENES, CSHL1_TARGET_GENES, DIDO1_TARGET_GENES, DLX2_TARGET_GENES, DYRK1A_TARGET_GENES, ERCC8_TARGET_GENES, FOXN3_TARGET_GENES, GLI4_TARGET_GENES, GUCY1B1_TARGET_GENES, HES2_TARGET_GENES, ID1_TARGET_GENES, IGLV5_37_TARGET_GENES, IRF5_TARGET_GENES, KAT5_TARGET_GENES, KLF7_TARGET_GENES, MEF2D_TARGET_GENES, OVOL3_TARGET_GENES, SALL4_TARGET_GENES, SKIL_TARGET_GENES, SNIP1_TARGET_GENES, TAF9B_TARGET_GENES, ZBTB12_TARGET_GENES, ZBTB18_TARGET_GENES, ZFP3_TARGET_GENES, ZNF146_TARGET_GENES, ZNF184_TARGET_GENES, ZNF22_TARGET_GENES, ZNF30_TARGET_GENES, ZNF302_TARGET_GENES, ZNF331_TARGET_GENES, ZNF33A_TARGET_GENES, ZNF350_TARGET_GENES, ZNF407_TARGET_GENES, ZNF488_TARGET_GENES, ZNF502_TARGET_GENES, ZNF510_TARGET_GENES, ZNF513_TARGET_GENES, ZNF558_TARGET_GENES, ZNF581_TARGET_GENES, ZNF596_TARGET_GENES, ZNF597_TARGET_GENES, ZNF664_TARGET_GENES, ZNF669_TARGET_GENES, ZNF8_TARGET_GENES, ZNF830_TARGET_GENES, ZNF843_TARGET_GENES, ZNF85_TARGET_GENES, ZSCAN31_TARGET_GENES, POU2AF1_TARGET_GENES, SETD1A_TARGET_GENES, TBX3_TARGET_GENES, ZNF623_TARGET_GENES, ZNF250_TARGET_GENES, MZF1_TARGET_GENES, LHX2_TARGET_GENES, FXR1_TARGET_GENES

ncRNA interactions

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

showing 2 of 23 interaction partners:

Partner	Partner type	Level	Source
C21orf49	lncRNA	RNA-Protein	High-throughput data
C21orf62-AS1	lncRNA	RNA-RNA	RISE database

Disease & clinical

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

Drugs & pharmacology

No curated drug or pharmacology associations for this gene.