PCAT19

Summary

PCAT19 (prostate cancer associated transcript 19, HGNC:49593) is a long non-coding RNA gene on chromosome 19q13.2.

At a glance

• Gene type: non-coding (lncRNA) — no protein product.
• GTEx eGene: eQTL in 46 tissues, sQTL in 47 (q < 0.05)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:49593
Approved symbol	PCAT19
Name	prostate cancer associated transcript 19
Location	19q13.2
Locus type	RNA, long non-coding
Status	Approved
Aliases	LINC01190
Ensembl gene	ENSG00000267107
Ensembl biotype	lncRNA
OMIM	618192
Entrez	100505495
RNAcentral	URS0000A776B1 — lncRNA, 3489 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 43 — 43 lncRNA

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

ENST00000588495, ENST00000594315, ENST00000595063, ENST00000595837, ENST00000597702, ENST00000598215, ENST00000599801, ENST00000650748, ENST00000650788, ENST00000650804, ENST00000650991, ENST00000651016, ENST00000651156, ENST00000651285, ENST00000651291, ENST00000651464, ENST00000651572, ENST00000651651, ENST00000651712, ENST00000651789, ENST00000651806, ENST00000651979, ENST00000652015, ENST00000652127, ENST00000652144, ENST00000652160, ENST00000652279, ENST00000652333, ENST00000652406, ENST00000652484, ENST00000652511, ENST00000652558, ENST00000656967, ENST00000664904, ENST00000668141, ENST00000783813, ENST00000783814, ENST00000783815, ENST00000783816, ENST00000783817, ENST00000783818, ENST00000783819, ENST00000783820

RefSeq mRNA: 0

Canonical transcript exons

ENST00000588495 — 4 exons

Exon	Start	End
ENSE00002843313	41479081	41479284
ENSE00002882507	41494540	41495427
ENSE00002888114	41454164	41456487
ENSE00002950105	41500584	41500644

Expression profiles

Bgee: expression breadth ubiquitous, 186 present calls, max score 96.77.

FANTOM5 (CAGE): breadth broad, TPM avg 2.6838 / max 108.7914, expressed in 308 samples.

Highest expression (Bgee): oviduct epithelium, lung, upper lobe of left lung, upper lobe of lung, uterine tube.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PCAT19 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 46 tissues and its splicing (sQTL) in 47 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 93 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Adipose Subcutaneous	sqtl	3.5e-239	-1.52	19:41495302:C:T
Muscle Skeletal	sqtl	4.5e-188	-1.41	19:41495302:C:T
Adipose Visceral Omentum	sqtl	7.6e-185	-1.53	19:41495302:C:T
Thyroid	sqtl	7.8e-184	-1.52	19:41495302:C:T
Lung	sqtl	1.1e-179	-1.53	19:41495302:C:T
Nerve Tibial	sqtl	7.3e-170	-1.51	19:41495302:C:T
Skin Sun Exposed Lower leg	sqtl	9.8e-159	-1.43	19:41495302:C:T
Esophagus Muscularis	sqtl	2.7e-158	-1.49	19:41495302:C:T
Esophagus Mucosa	sqtl	1.4e-138	-1.48	19:41495302:C:T
Breast Mammary Tissue	sqtl	1.9e-136	-1.54	19:41495302:C:T
Skin Not Sun Exposed Suprapubic	sqtl	5.9e-135	-1.36	19:41495302:C:T
Colon Transverse	sqtl	7.3e-126	-1.44	19:41495302:C:T
Artery Tibial	sqtl	6.2e-125	+1.19	19:41495302:C:T
Heart Left Ventricle	sqtl	5.1e-104	-1.62	19:41495302:C:T
Heart Atrial Appendage	sqtl	1.7e-99	-1.52	19:41495302:C:T
Adipose Subcutaneous	eqtl	5.8e-98	-0.55	19:41495302:C:T
Stomach	sqtl	1.4e-93	-1.38	19:41495302:C:T
Esophagus Gastroesophageal Junction	sqtl	4.2e-93	-1.50	19:41495302:C:T
Colon Sigmoid	sqtl	5.1e-93	-1.46	19:41495302:C:T
Artery Aorta	sqtl	2.4e-88	-1.33	19:41495302:C:T

FANTOM5 promoters

6 alternative TSS:

Promoter ID	TPM avg	Samples expressed
181072	1.2188	208
181074	0.8942	176
181073	0.3818	75
181071	0.0963	56
181069	0.0806	13
181070	0.0121	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oviduct epithelium	UBERON:0004804	96.77	gold quality
right lung	UBERON:0002167	96.42	gold quality
upper lobe of left lung	UBERON:0008952	93.28	gold quality
upper lobe of lung	UBERON:0008948	92.64	gold quality
right uterine tube	UBERON:0001302	92.34	gold quality
omental fat pad	UBERON:0010414	91.79	gold quality
peritoneum	UBERON:0002358	91.75	gold quality
adipose tissue of abdominal region	UBERON:0007808	91.10	gold quality
fallopian tube	UBERON:0003889	90.14	gold quality
lung	UBERON:0002048	89.09	gold quality
subcutaneous adipose tissue	UBERON:0002190	89.01	gold quality
apex of heart	UBERON:0002098	88.94	gold quality
spleen	UBERON:0002106	88.53	gold quality
adipose tissue	UBERON:0001013	87.04	gold quality
heart left ventricle	UBERON:0002084	85.88	gold quality
cardiac ventricle	UBERON:0002082	85.31	gold quality
left lobe of thyroid gland	UBERON:0001120	84.56	gold quality
thyroid gland	UBERON:0002046	84.23	gold quality
left uterine tube	UBERON:0001303	84.08	gold quality
right lobe of thyroid gland	UBERON:0001119	83.73	gold quality
colonic epithelium	UBERON:0000397	83.24	gold quality
heart	UBERON:0000948	83.22	gold quality
right atrium auricular region	UBERON:0006631	83.05	gold quality
endocervix	UBERON:0000458	83.02	gold quality
hindlimb stylopod muscle	UBERON:0004252	82.77	gold quality
smooth muscle tissue	UBERON:0001135	82.44	gold quality
body of uterus	UBERON:0009853	82.37	gold quality
cardiac atrium	UBERON:0002081	82.29	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	82.01	gold quality
visceral pleura	UBERON:0002401	81.16	gold quality
buccal mucosa cell	CL:0002336	80.97	gold quality
lower esophagus muscularis layer	UBERON:0035833	80.94	gold quality
lower esophagus	UBERON:0013473	80.89	gold quality
endometrium	UBERON:0001295	80.62	gold quality
calcaneal tendon	UBERON:0003701	80.49	gold quality
left ovary	UBERON:0002119	80.46	gold quality
tibial nerve	UBERON:0001323	80.37	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	80.36	gold quality
metanephros cortex	UBERON:0010533	79.84	gold quality
uterus	UBERON:0000995	79.76	gold quality
left coronary artery	UBERON:0001626	79.52	gold quality
islet of Langerhans	UBERON:0000006	79.00	gold quality
ectocervix	UBERON:0012249	78.94	gold quality
muscle of leg	UBERON:0001383	78.92	gold quality
lower lobe of lung	UBERON:0008949	78.75	gold quality
gastrocnemius	UBERON:0001388	78.59	gold quality
coronary artery	UBERON:0001621	78.55	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.40	gold quality
female reproductive system	UBERON:0000474	78.25	gold quality
uterine cervix	UBERON:0000002	78.14	gold quality
lower esophagus mucosa	UBERON:0035834	77.85	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	77.82	gold quality
right ovary	UBERON:0002118	77.55	gold quality
vagina	UBERON:0000996	77.46	gold quality
esophagus	UBERON:0001043	77.25	gold quality
myometrium	UBERON:0001296	77.15	gold quality
vermiform appendix	UBERON:0001154	76.92	gold quality
muscle layer of sigmoid colon	UBERON:0035805	76.92	gold quality
adult mammalian kidney	UBERON:0000082	76.56	gold quality
lymph node	UBERON:0000029	76.55	gold quality
ovary	UBERON:0000992	76.53	gold quality
skin of leg	UBERON:0001511	76.49	gold quality
mucosa of transverse colon	UBERON:0004991	76.44	gold quality
parietal pleura	UBERON:0002400	76.21	gold quality
right coronary artery	UBERON:0001625	76.19	gold quality
cardiac muscle of right atrium	UBERON:0003379	75.95	gold quality
skin of abdomen	UBERON:0001416	75.89	gold quality
bronchial epithelial cell	CL:0002328	75.85	gold quality
gall bladder	UBERON:0002110	75.79	gold quality
metanephros	UBERON:0000081	75.72	gold quality
prostate gland	UBERON:0002367	75.68	gold quality
spinal cord	UBERON:0002240	75.65	gold quality
left ventricle myocardium	UBERON:0006566	75.48	gold quality
small intestine Peyer’s patch	UBERON:0003454	75.39	gold quality
left adrenal gland cortex	UBERON:0035825	75.38	gold quality
mucosa of stomach	UBERON:0001199	75.30	gold quality
right adrenal gland	UBERON:0001233	75.07	gold quality
bronchus	UBERON:0002185	74.99	gold quality
hypothalamus	UBERON:0001898	74.91	gold quality
left adrenal gland	UBERON:0001234	74.79	gold quality
right adrenal gland cortex	UBERON:0035827	74.78	gold quality
placenta	UBERON:0001987	74.74	gold quality
tendon	UBERON:0000043	74.64	gold quality
zone of skin	UBERON:0000014	74.62	gold quality
adenohypophysis	UBERON:0002196	74.51	gold quality
right lobe of liver	UBERON:0001114	74.44	gold quality
adrenal gland	UBERON:0002369	74.40	gold quality
tibial artery	UBERON:0007610	74.40	gold quality
popliteal artery	UBERON:0002250	74.34	gold quality
anterior cingulate cortex	UBERON:0009835	74.27	gold quality
esophagus mucosa	UBERON:0002469	74.12	gold quality
body of stomach	UBERON:0001161	74.06	gold quality
adrenal cortex	UBERON:0001235	73.90	gold quality
minor salivary gland	UBERON:0001830	73.90	gold quality
aorta	UBERON:0000947	73.73	gold quality
small intestine	UBERON:0002108	73.69	gold quality
amygdala	UBERON:0001876	73.68	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.46	gold quality
ascending aorta	UBERON:0001496	73.42	gold quality
pancreas	UBERON:0001264	73.36	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-CURD-126	yes	1119.78
E-MTAB-10662	yes	744.10
E-MTAB-10287	yes	74.72
E-ANND-3	yes	32.13

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 6)

• rs11672691, a Prostate Cancer (PCa) risk SNP, has been associated with the diagnosis of aggressive and fatal PCa. Patients with homozygous risk allele genotype G showed significantly shorter biochemical recurrence-free survival compared to patients with the non-risk allele genotype A (p = 0.032), suggesting a role for the risk SNP in disease progression after local therapy. (PMID:30033362)
• lncRNA PCAT19 promotes the proliferation of laryngocarcinoma cells via modulation of the miR-182/PDK4 axis. (PMID:30868666)
• Suppression of long non-coding RNA PCAT19 inhibits glioma cell proliferation and invasion, and increases cell apoptosis through regulation of MELK targeted by miR-142-5p. (PMID:32980991)
• PCAT19 Regulates the Proliferation and Apoptosis of Lung Cancer Cells by Inhibiting miR-25-3p via Targeting the MAP2K4 Signal Axis. (PMID:35615401)
• Long Non-Coding RNA PCAT19 Regulates the Malignant Progression of Bladder Cancer through the miR-335-5p/IER2 Axis. (PMID:36017918)
• Inhibition of lncRNA PCAT19 promotes breast cancer proliferation. (PMID:36992525)

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
B3GNT8	protein-coding	374907
DMAC2	protein-coding	55101
ERICH4	protein-coding	100170765
LINC01480	ncRNA	101927931
CEACAM21	protein-coding	90273

Protein

Non-coding RNA — no protein product.

Function

Gene-set membership (MSigDB)

This non-coding RNA is a member of 41 curated MSigDB gene sets — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data).

LCORL_TARGET_GENES, LHX9_TARGET_GENES, MAFG_TARGET_GENES, ZNF184_TARGET_GENES, ZNF362_TARGET_GENES, ZNF491_TARGET_GENES, ZNF577_TARGET_GENES, ZNF660_TARGET_GENES, ZSCAN21_TARGET_GENES, GSE13485_CTRL_VS_DAY1_YF17D_VACCINE_PBMC_DN, FAN_EMBRYONIC_CTX_BIG_GROUPS_BRAIN_ENDOTHELIAL, FAN_EMBRYONIC_CTX_BRAIN_ENDOTHELIAL_1, MANNO_MIDBRAIN_NEUROTYPES_HENDO, AIZARANI_LIVER_C10_MVECS_1, AIZARANI_LIVER_C13_LSECS_2, GAO_LARGE_INTESTINE_24W_C2_MKI67POS_PROGENITOR, GAO_LARGE_INTESTINE_ADULT_CJ_IMMUNE_CELLS, MURARO_PANCREAS_ENDOTHELIAL_CELL, DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_PERICYTES, CUI_DEVELOPING_HEART_C4_ENDOTHELIAL_CELL, DESCARTES_FETAL_ADRENAL_VASCULAR_ENDOTHELIAL_CELLS, DESCARTES_FETAL_CEREBELLUM_VASCULAR_ENDOTHELIAL_CELLS, DESCARTES_FETAL_CEREBRUM_VASCULAR_ENDOTHELIAL_CELLS, DESCARTES_FETAL_EYE_VASCULAR_ENDOTHELIAL_CELLS, DESCARTES_FETAL_KIDNEY_VASCULAR_ENDOTHELIAL_CELLS, DESCARTES_FETAL_LIVER_VASCULAR_ENDOTHELIAL_CELLS, DESCARTES_FETAL_THYMUS_VASCULAR_ENDOTHELIAL_CELLS, MZF1_TARGET_GENES, TRAVAGLINI_LUNG_CILIATED_CELL, TRAVAGLINI_LUNG_PROXIMAL_CILIATED_CELL, TRAVAGLINI_LUNG_CAPILLARY_INTERMEDIATE_2_CELL, FAN_OVARY_CL7_ANGEIOGENIC_ENDOTHELIAL_CELL, FAN_OVARY_CL9_PUTATIVE_APOPTOTIC_ENDOTHELIAL_CELL, JONES_OVARY_ENDOTHELIAL, JONES_OVARY_NK_CELL, JONES_OVARY_MACROPHAGE, SU_HO_FOETAL_FEMUR_C5_ENDOTHELIAL_CELL, SU_HO_CONV_CENT_CHONDROSARCOMA_STROMAL_C6_ENDOTHELIAL_CELL, chr19q13, GSE16385_UNTREATED_VS_12H_IFNG_TNF_TREATED_MACROPHAGE_UP, GSE41867_NAIVE_VS_DAY15_LCMV_CONE13_EFFECTOR_CD8_TCELL_UP

ncRNA interactions

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

showing 10 of 12 interaction partners:

Partner	Partner type	Level	Source
A1CF	protein	RNA-Protein	High-throughput data
AGO1	protein	RNA-Protein	High-throughput data
IGF2BP3	protein	RNA-Protein	High-throughput data
SOX2	protein	RNA-Protein	High-throughput data
IGF2BP1	protein	RNA-Protein	High-throughput data
AGO2	protein	RNA-Protein	High-throughput data
FTO	protein	RNA-Protein	High-throughput data
DHX36	protein	RNA-Protein	High-throughput data
miR-143-3p	miRNA	RNA-RNA	Literature mining
miR-142-5p	miRNA	RNA-RNA	Literature mining

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.

8 ncRNA–disease associations:

Disease	Causal?	Validated by
Glioma	Yes	Western Blot, CCK8, qRT-PCR, RIP, Flow Cytometry, Luciferase Report Assay, Colony Formation Assay, Transwell Assay
Carcinoma, Non-Small-Cell Lung	No	qRT-PCR, Microarray
Carcinoma, Non-Small-Cell Lung	Yes	CCK8, qRT-PCR, Western Blot
Esophageal Squamous Cell Carcinoma	No	qRT-PCR, RNA-seq
Stomach Neoplasms	Yes	Western Blot, Invasion Assay, CCK8, qRT-PCR, Flow Cytometry, FISH, Luciferase Report Assay, IHC, EdU Staining, Transwell Assay
Laryngeal Neoplasms	Yes	qRT-PCR
Urinary Bladder Neoplasms	Yes	qRT-PCR, MTT
Neuralgia	Yes	In Vivo Experiment, RNA Pull-Down, Western Blot, Transfection, qRT-PCR, RIP, ELISA

Drugs & pharmacology

ncRNA–drug associations

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

3 ncRNA–drug associations:

Drug	Relation	Effect	Condition
Cisplatin	drug_resistance	resistant	cell line (SKOV3)
Radioactivity Iodine	drug_resistance	sensitive	tissue
Paclitaxel	drug_resistance	resistant	cell line (SKOV3)