PRRT3-AS1

Summary

PRRT3-AS1 (PRRT3 antisense RNA 1, HGNC:41151) is a long non-coding RNA gene on chromosome 3p25.3.

At a glance

• Gene type: non-coding (lncRNA) — no protein product.
• Sense gene: antisense to PRRT3 — the sense gene carries 165 ClinVar variants (the sense gene’s biology, not this transcript’s)
• GTEx eGene: eQTL in 15 tissues, sQTL in 5 (q < 0.05)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:41151
Approved symbol	PRRT3-AS1
Name	PRRT3 antisense RNA 1
Location	3p25.3
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000230082
Ensembl biotype	lncRNA
OMIM	619106
Entrez	100874032
RNAcentral	URS0000008D1D — lncRNA, 614 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 lncRNA

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

ENST00000431558, ENST00000773194, ENST00000773195, ENST00000773196, ENST00000773197, ENST00000773198

RefSeq mRNA: 0

Canonical transcript exons

ENST00000431558 — 4 exons

Exon	Start	End
ENSE00001613089	9948067	9948180
ENSE00001638215	9948355	9948469
ENSE00004137949	9954604	9954793
ENSE00004137951	9947357	9947604

Expression profiles

Bgee: expression breadth ubiquitous, 215 present calls, max score 85.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.5542 / max 54.5147, expressed in 963 samples.

Highest expression (Bgee): hindlimb stylopod muscle, gastrocnemius, muscle of leg, tibialis anterior, male germ line stem cell (sensu Vertebrata) in testis.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PRRT3-AS1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 15 tissues and its splicing (sQTL) in 5 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

20 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Liver	sqtl	4.0e-32	+1.08	3:9939477:C:T
Whole Blood	sqtl	3.2e-16	+0.50	3:9939821:C:A
Spleen	sqtl	1.1e-14	+0.97	3:9940229:C:G
Cells Cultured fibroblasts	eqtl	2.8e-13	+0.25	3:9933702:C:G
Small Intestine Terminal Ileum	sqtl	6.5e-10	+0.86	3:9939437:G:A
Esophagus Muscularis	eqtl	5.7e-06	+0.27	3:9933702:C:G
Adipose Subcutaneous	eqtl	1.2e-05	-0.20	3:10037010:G:GT
Skin Sun Exposed Lower leg	eqtl	2.0e-04	+0.27	3:9933702:C:G
Skin Not Sun Exposed Suprapubic	eqtl	9.2e-04	-0.20	3:9922760:A:G
Colon Transverse	eqtl	9.6e-03	-0.47	3:9857275:C:T
Whole Blood	eqtl	1.2e-02	-0.68	3:9334335:C:T
Heart Left Ventricle	eqtl	1.7e-02	+0.29	3:9933702:C:G
Adipose Visceral Omentum	eqtl	1.9e-02	+0.15	3:9933702:C:G
Artery Tibial	eqtl	2.0e-02	-0.35	3:10073349:G:T
Cells EBV-transformed lymphocytes	eqtl	2.6e-02	-0.39	3:9341279:C:T
Muscle Skeletal	eqtl	3.4e-02	+0.11	3:9933702:C:G
Brain Caudate basal ganglia	eqtl	4.1e-02	-1.53	3:10932239:A:G
Brain Anterior cingulate cortex BA24	eqtl	4.2e-02	-0.92	3:9701463:A:C
Brain Cerebellum	sqtl	4.4e-02	-0.51	3:9972487:C:T
Stomach	eqtl	4.5e-02	-0.40	3:8952085:G:A

FANTOM5 promoters

1 alternative TSS:

Promoter ID	TPM avg	Samples expressed
35264	2.5542	963

Top tissues by expression

showing 100 of 241 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
hindlimb stylopod muscle	UBERON:0004252	85.62	gold quality
gastrocnemius	UBERON:0001388	85.10	gold quality
muscle of leg	UBERON:0001383	84.11	gold quality
tibialis anterior	UBERON:0001385	83.50	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.98	silver quality
deltoid	UBERON:0001476	82.85	gold quality
quadriceps femoris	UBERON:0001377	82.40	silver quality
vastus lateralis	UBERON:0001379	81.68	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	80.16	gold quality
left ventricle myocardium	UBERON:0006566	79.92	gold quality
skeletal muscle tissue	UBERON:0001134	78.48	gold quality
biceps brachii	UBERON:0001507	78.03	gold quality
muscle tissue	UBERON:0002385	77.63	gold quality
adipose tissue	UBERON:0001013	77.24	gold quality
adipose tissue of abdominal region	UBERON:0007808	76.64	gold quality
omental fat pad	UBERON:0010414	76.18	gold quality
peritoneum	UBERON:0002358	76.13	gold quality
ileal mucosa	UBERON:0000331	74.90	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	74.86	gold quality
sural nerve	UBERON:0015488	74.71	gold quality
mucosa of transverse colon	UBERON:0004991	74.70	gold quality
subcutaneous adipose tissue	UBERON:0002190	74.63	gold quality
left coronary artery	UBERON:0001626	74.55	gold quality
tibial nerve	UBERON:0001323	74.39	gold quality
coronary artery	UBERON:0001621	74.00	gold quality
body of pancreas	UBERON:0001150	73.99	gold quality
germinal epithelium of ovary	UBERON:0001304	73.72	silver quality
colonic epithelium	UBERON:0000397	72.57	gold quality
mucosa of paranasal sinus	UBERON:0005030	72.19	gold quality
muscle layer of sigmoid colon	UBERON:0035805	72.13	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	71.82	gold quality
right coronary artery	UBERON:0001625	71.70	gold quality
right adrenal gland	UBERON:0001233	71.64	gold quality
left ovary	UBERON:0002119	71.48	gold quality
lower esophagus	UBERON:0013473	71.05	gold quality
lower esophagus muscularis layer	UBERON:0035833	71.05	gold quality
right ovary	UBERON:0002118	70.87	gold quality
popliteal artery	UBERON:0002250	70.83	gold quality
tibial artery	UBERON:0007610	70.80	gold quality
aorta	UBERON:0000947	70.62	gold quality
cardiac atrium	UBERON:0002081	70.54	gold quality
thoracic aorta	UBERON:0001515	70.51	gold quality
right adrenal gland cortex	UBERON:0035827	70.47	gold quality
ascending aorta	UBERON:0001496	70.46	gold quality
apex of heart	UBERON:0002098	70.40	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	70.29	gold quality
cortical plate	UBERON:0005343	70.27	gold quality
right atrium auricular region	UBERON:0006631	70.25	gold quality
body of uterus	UBERON:0009853	70.09	gold quality
descending thoracic aorta	UBERON:0002345	69.96	gold quality
ovary	UBERON:0000992	69.68	gold quality
bone marrow cell	CL:0002092	69.33	silver quality
spinal cord	UBERON:0002240	69.22	gold quality
pancreatic ductal cell	CL:0002079	69.08	silver quality
pancreas	UBERON:0001264	69.03	gold quality
esophagus	UBERON:0001043	68.99	gold quality
left adrenal gland cortex	UBERON:0035825	68.91	gold quality
rectum	UBERON:0001052	68.82	gold quality
left adrenal gland	UBERON:0001234	68.71	gold quality
adrenal cortex	UBERON:0001235	68.56	gold quality
left uterine tube	UBERON:0001303	68.46	gold quality
lower esophagus mucosa	UBERON:0035834	68.42	gold quality
prostate gland	UBERON:0002367	68.33	gold quality
adrenal gland	UBERON:0002369	68.27	gold quality
thoracic mammary gland	UBERON:0005200	68.20	gold quality
fundus of stomach	UBERON:0001160	68.04	gold quality
mammary gland	UBERON:0001911	68.01	gold quality
colon	UBERON:0001155	67.93	gold quality
heart	UBERON:0000948	67.85	gold quality
large intestine	UBERON:0000059	67.63	gold quality
vagina	UBERON:0000996	67.55	gold quality
transverse colon	UBERON:0001157	67.53	gold quality
esophagus mucosa	UBERON:0002469	67.39	gold quality
body of stomach	UBERON:0001161	67.33	gold quality
smooth muscle tissue	UBERON:0001135	67.10	gold quality
heart left ventricle	UBERON:0002084	66.81	gold quality
myometrium	UBERON:0001296	66.67	gold quality
endocervix	UBERON:0000458	66.64	gold quality
endothelial cell	CL:0000115	66.49	gold quality
tendon	UBERON:0000043	66.46	gold quality
cardiac ventricle	UBERON:0002082	66.45	gold quality
stomach	UBERON:0000945	66.19	gold quality
minor salivary gland	UBERON:0001830	66.09	gold quality
uterine cervix	UBERON:0000002	66.08	gold quality
urinary bladder	UBERON:0001255	65.99	gold quality
intestine	UBERON:0000160	65.98	gold quality
ectocervix	UBERON:0012249	65.83	gold quality
granulocyte	CL:0000094	65.76	gold quality
tendon of biceps brachii	UBERON:0008188	65.56	gold quality
right lobe of thyroid gland	UBERON:0001119	65.43	gold quality
kidney epithelium	UBERON:0004819	65.37	gold quality
female reproductive system	UBERON:0000474	65.23	gold quality
calcaneal tendon	UBERON:0003701	65.13	gold quality
cerebellar cortex	UBERON:0002129	65.10	gold quality
mucosa of stomach	UBERON:0001199	65.08	gold quality
cerebellar hemisphere	UBERON:0002245	65.04	gold quality
saliva-secreting gland	UBERON:0001044	64.91	gold quality
mouth mucosa	UBERON:0003729	64.90	gold quality
uterus	UBERON:0000995	64.88	gold quality
multicellular organism	UBERON:0000468	64.85	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.27

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• Long non-coding RNA PRRT3-AS1 silencing inhibits prostate cancer cell proliferation and promotes apoptosis and autophagy. (PMID:32086850)
• The integration of single-cell sequencing, TCGA, and GEO data analysis revealed that PRRT3-AS1 is a biomarker and therapeutic target of SKCM. (PMID:36211371)
• LncRNA PRRT3-AS1 exerts oncogenic effects on nonsmall cell lung cancer by targeting microRNA-507/homeobox B5 axis. (PMID:37304647)

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
PRRT3	protein-coding	285368
EMC3-AS1	ncRNA	442075
EMC3	protein-coding	55831
CRELD1	protein-coding	78987
IL17RE	protein-coding	132014
JAGN1	protein-coding	84522
IL17RC	protein-coding	84818

Protein

Non-coding RNA — no protein product.

Function

Gene-set membership (MSigDB)

This non-coding RNA is a member of 16 curated MSigDB gene sets — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data).

KOYAMA_SEMA3B_TARGETS_DN, FEV_TARGET_GENES, KAT2A_TARGET_GENES, SNRNP70_TARGET_GENES, SUPT16H_TARGET_GENES, UBN1_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF30_TARGET_GENES, ZNF329_TARGET_GENES, ZNF423_TARGET_GENES, ZSCAN30_TARGET_GENES, ZSCAN31_TARGET_GENES, BLANCO_MELO_BETA_INTERFERON_TREATED_BRONCHIAL_EPITHELIAL_CELLS_DN, ZBTB44_TARGET_GENES, ZNF224_TARGET_GENES, chr3p25

ncRNA interactions

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

showing 60 of 82 interaction partners:

Partner	Partner type	Level	Source
hsa-miR-106a-3p	miRNA	RNA-RNA	Literature mining
WDR33	protein	RNA-Protein	High-throughput data
RBM6	protein	RNA-Protein	High-throughput data combine LncPro prediction
UPF1	protein	RNA-Protein	High-throughput data
hnRNPA2B1	protein	RNA-Protein	High-throughput data
FUS	protein	RNA-Protein	High-throughput data
BCCIP	protein	RNA-Protein	ENCODE
BUD13	protein	RNA-Protein	ENCODE
CSTF2	protein	RNA-Protein	ENCODE
CSTF2T	protein	RNA-Protein	ENCODE
DDX55	protein	RNA-Protein	ENCODE
DDX59	protein	RNA-Protein	ENCODE
DGCR8	protein	RNA-Protein	ENCODE
DHX30	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
GRSF1	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
hnRNPM	protein	RNA-Protein	ENCODE
HNRNPU	protein	RNA-Protein	ENCODE
IF2B1	protein	RNA-Protein	ENCODE
IGF2BP3	protein	RNA-Protein	ENCODE;GSE78507
ILF3	protein	RNA-Protein	ENCODE
LARP4	protein	RNA-Protein	ENCODE
LSM11	protein	RNA-Protein	ENCODE
MATR3	protein	RNA-Protein	ENCODE
NCBP2	protein	RNA-Protein	ENCODE
NKRF	protein	RNA-Protein	ENCODE
PCBP2	protein	RNA-Protein	ENCODE
PPIG	protein	RNA-Protein	ENCODE
PRP17	protein	RNA-Protein	ENCODE
PRPF8	protein	RNA-Protein	ENCODE
PTBP1	protein	RNA-Protein	ENCODE
QKI	protein	RNA-Protein	ENCODE
RBM15	protein	RNA-Protein	ENCODE
RBM22	protein	RNA-Protein	ENCODE
RBM5	protein	RNA-Protein	ENCODE
TAF15	protein	RNA-Protein	ENCODE
RNC	protein	RNA-Protein	ENCODE
Ro60	protein	RNA-Protein	ENCODE
HNRNPA1	protein	RNA-Protein	ENCODE
RPB7	protein	RNA-Protein	ENCODE
RPS3	protein	RNA-Protein	ENCODE
SAP49	protein	RNA-Protein	ENCODE
PSF	protein	RNA-Protein	ENCODE;GSE90650
SLTM	protein	RNA-Protein	ENCODE
SND1	protein	RNA-Protein	ENCODE
SFRS1	protein	RNA-Protein	ENCODE
SUGP2	protein	RNA-Protein	ENCODE
TIA1	protein	RNA-Protein	ENCODE
U2AF1	protein	RNA-Protein	ENCODE
U2AF2	protein	RNA-Protein	ENCODE
U5S1	protein	RNA-Protein	ENCODE

Disease & clinical

ncRNA disease associations

Curated non-coding-RNA → disease associations (LncRNADisease, HMDD) — these are RNA-level associations for this gene, not the positional variant data omitted above.

1 ncRNA–disease associations:

Disease	Causal?	Validated by
Esophageal Squamous Cell Carcinoma	No	qRT-PCR, RNA-seq

Drugs & pharmacology

ncRNA–drug associations

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

3 ncRNA–drug associations:

Drug	Relation	Effect	Condition
Paclitaxel	drug_resistance	resistant	tissue
Panobinostat	drug_target	down-regulated	“cell line (SK-NEP-1, G401)”
Temozolomide	drug_resistance	sensitive	cell line (U251)