PRDM4-AS1

Summary

PRDM4-AS1 (PRDM4 antisense RNA 1, HGNC:56186) is a long non-coding RNA gene on chromosome 12q23.3.

At a glance

• Gene type: non-coding (lncRNA) — no protein product.
• Sense gene: antisense to PRDM4 — the sense gene carries 3 GWAS associations, 119 ClinVar variants (the sense gene’s biology, not this transcript’s)
• GTEx eGene: eQTL in 7 tissues, sQTL in 1 (q < 0.05)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:56186
Approved symbol	PRDM4-AS1
Name	PRDM4 antisense RNA 1
Location	12q23.3
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000258136
Ensembl biotype	lncRNA
Entrez	101929162
RNAcentral	URS0000759A13 — lncRNA, 1714 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 lncRNA

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

ENST00000546714, ENST00000546829

RefSeq mRNA: 0

Canonical transcript exons

ENST00000546714 — 5 exons

Exon	Start	End
ENSE00002335341	107738022	107738489
ENSE00002335505	107758275	107758392
ENSE00002378948	107759772	107759968
ENSE00002387922	107739127	107739664
ENSE00002429564	107736589	107736947

Expression profiles

Bgee: expression breadth ubiquitous, 153 present calls, max score 85.14.

Highest expression (Bgee): primordial germ cell in gonad, male germ line stem cell (sensu Vertebrata) in testis, sperm, bone marrow cell, colonic epithelium.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PRDM4-AS1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 7 tissues and its splicing (sQTL) in 1 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

8 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Testis	sqtl	6.6e-36	+0.96	12:107679918:A:G
Testis	eqtl	1.1e-07	+0.18	12:107756981:C:A
Brain Anterior cingulate cortex BA24	eqtl	3.2e-03	-0.38	12:106988381:G:A
Pituitary	eqtl	5.5e-03	+0.30	12:107766675:C:T
Thyroid	eqtl	3.3e-02	+0.34	12:108469450:A:C
Cells Cultured fibroblasts	eqtl	3.8e-02	+0.16	12:107752695:A:G
Stomach	eqtl	4.4e-02	+0.21	12:107752695:A:G
Brain Nucleus accumbens basal ganglia	eqtl	4.9e-02	+1.56	12:107918371:C:G

Top tissues by expression

showing 100 of 242 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.14	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.12	gold quality
sperm	CL:0000019	71.55	silver quality
bone marrow cell	CL:0002092	66.85	silver quality
colonic epithelium	UBERON:0000397	66.18	silver quality
left testis	UBERON:0004533	63.90	gold quality
right testis	UBERON:0004534	63.46	gold quality
lower esophagus mucosa	UBERON:0035834	63.46	gold quality
testis	UBERON:0000473	62.55	gold quality
stromal cell of endometrium	CL:0002255	62.32	gold quality
ventricular zone	UBERON:0003053	62.26	gold quality
adrenal tissue	UBERON:0018303	60.62	gold quality
rectum	UBERON:0001052	60.51	gold quality
granulocyte	CL:0000094	60.21	gold quality
esophagus mucosa	UBERON:0002469	59.34	gold quality
small intestine Peyer’s patch	UBERON:0003454	59.33	gold quality
apex of heart	UBERON:0002098	59.17	gold quality
ganglionic eminence	UBERON:0004023	59.06	gold quality
right adrenal gland cortex	UBERON:0035827	58.67	gold quality
small intestine	UBERON:0002108	57.93	gold quality
right adrenal gland	UBERON:0001233	57.91	gold quality
leukocyte	CL:0000738	57.69	gold quality
transverse colon	UBERON:0001157	57.55	gold quality
body of pancreas	UBERON:0001150	57.45	gold quality
monocyte	CL:0000576	57.34	gold quality
left adrenal gland cortex	UBERON:0035825	57.33	gold quality
esophagus	UBERON:0001043	57.21	gold quality
metanephros cortex	UBERON:0010533	57.11	gold quality
left adrenal gland	UBERON:0001234	57.03	gold quality
vermiform appendix	UBERON:0001154	56.90	gold quality
body of stomach	UBERON:0001161	56.50	gold quality
adrenal gland	UBERON:0002369	56.42	gold quality
adrenal cortex	UBERON:0001235	56.39	gold quality
pancreas	UBERON:0001264	55.84	gold quality
stomach	UBERON:0000945	55.62	gold quality
mucosa of stomach	UBERON:0001199	55.41	gold quality
calcaneal tendon	UBERON:0003701	55.31	silver quality
cortex of kidney	UBERON:0001225	54.90	gold quality
hindlimb stylopod muscle	UBERON:0004252	54.87	silver quality
esophagogastric junction muscularis propria	UBERON:0035841	54.86	gold quality
lower esophagus	UBERON:0013473	54.82	gold quality
lymph node	UBERON:0000029	54.81	gold quality
gall bladder	UBERON:0002110	54.75	gold quality
lower esophagus muscularis layer	UBERON:0035833	54.73	gold quality
intestine	UBERON:0000160	54.69	gold quality
body of uterus	UBERON:0009853	54.35	gold quality
spleen	UBERON:0002106	54.21	gold quality
smooth muscle tissue	UBERON:0001135	54.01	gold quality
minor salivary gland	UBERON:0001830	53.99	gold quality
vagina	UBERON:0000996	53.93	gold quality
colon	UBERON:0001155	53.87	gold quality
muscle layer of sigmoid colon	UBERON:0035805	53.84	gold quality
tonsil	UBERON:0002372	53.77	gold quality
omental fat pad	UBERON:0010414	53.75	gold quality
peritoneum	UBERON:0002358	53.71	gold quality
islet of Langerhans	UBERON:0000006	53.52	gold quality
large intestine	UBERON:0000059	53.49	gold quality
right lobe of liver	UBERON:0001114	53.49	gold quality
skin of abdomen	UBERON:0001416	53.48	gold quality
descending thoracic aorta	UBERON:0002345	53.34	gold quality
caecum	UBERON:0001153	53.20	gold quality
adipose tissue of abdominal region	UBERON:0007808	53.03	gold quality
adult mammalian kidney	UBERON:0000082	53.00	gold quality
subcutaneous adipose tissue	UBERON:0002190	52.60	gold quality
endometrium	UBERON:0001295	52.58	gold quality
uterine cervix	UBERON:0000002	52.32	gold quality
saliva-secreting gland	UBERON:0001044	52.24	gold quality
mouth mucosa	UBERON:0003729	52.19	gold quality
metanephros	UBERON:0000081	52.12	gold quality
mucosa of transverse colon	UBERON:0004991	52.10	gold quality
uterus	UBERON:0000995	52.07	gold quality
cerebellar cortex	UBERON:0002129	52.01	gold quality
cerebellar hemisphere	UBERON:0002245	51.99	gold quality
left coronary artery	UBERON:0001626	51.89	gold quality
left ovary	UBERON:0002119	51.89	gold quality
right lobe of thyroid gland	UBERON:0001119	51.88	gold quality
heart left ventricle	UBERON:0002084	51.83	gold quality
right hemisphere of cerebellum	UBERON:0014890	51.80	gold quality
left lobe of thyroid gland	UBERON:0001120	51.77	gold quality
thyroid gland	UBERON:0002046	51.51	gold quality
right ovary	UBERON:0002118	51.49	gold quality
endocervix	UBERON:0000458	51.43	gold quality
cardiac ventricle	UBERON:0002082	51.40	gold quality
thoracic aorta	UBERON:0001515	51.30	gold quality
blood	UBERON:0000178	51.22	silver quality
ascending aorta	UBERON:0001496	51.19	gold quality
cerebellum	UBERON:0002037	51.13	gold quality
prefrontal cortex	UBERON:0000451	50.98	gold quality
coronary artery	UBERON:0001621	50.95	gold quality
female reproductive system	UBERON:0000474	50.88	gold quality
kidney	UBERON:0002113	50.81	gold quality
anatomical system	UBERON:0000467	50.70	gold quality
upper lobe of left lung	UBERON:0008952	50.70	gold quality
heart	UBERON:0000948	50.60	gold quality
tibial nerve	UBERON:0001323	50.55	gold quality
material anatomical entity	UBERON:0000465	50.49	gold quality
multicellular organism	UBERON:0000468	50.48	gold quality
ectocervix	UBERON:0012249	50.39	gold quality
zone of skin	UBERON:0000014	50.24	gold quality
adipose tissue	UBERON:0001013	50.23	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.46

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
PRDM4	protein-coding	11108
PWP1	protein-coding	11137
ASCL4	protein-coding	121549
ABTB3	protein-coding	121551

Protein

Non-coding RNA — no protein product.

Function

Gene-set membership (MSigDB)

This non-coding RNA is a member of 1 curated MSigDB gene set — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data).

chr12q23

Disease & clinical

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

Drugs & pharmacology

No curated drug or pharmacology associations for this gene.