PCAT19 (prostate cancer associated transcript 19) - Rat Genome Database

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Gene: PCAT19 (prostate cancer associated transcript 19) Homo sapiens
Analyze
Symbol: PCAT19
Name: prostate cancer associated transcript 19
RGD ID: 7943681
HGNC Page HGNC:49593
Description: INTERACTS WITH 4,4'-sulfonyldiphenol; bisphenol A; fipronil
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LINC01190; prostate cancer associated transcript 19 (non-protein coding)
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381941,454,169 - 41,500,649 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1941,449,520 - 41,501,255 (-)EnsemblGRCh38hg38GRCh38
GRCh371941,960,074 - 42,006,559 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera1938,755,282 - 38,806,407 (-)NCBICelera
Cytogenetic Map19q13.2NCBI
HuRef1938,391,679 - 38,438,155 (-)NCBIHuRef
CHM1_11941,959,704 - 42,006,179 (-)NCBICHM1_1
T2T-CHM13v2.01944,275,440 - 44,321,937 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:12477932   PMID:23065704   PMID:24497837   PMID:30033362   PMID:30868666   PMID:32980991   PMID:35615401   PMID:36017918   PMID:36992525  


Genomics

Variants

.
Variants in PCAT19
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19p13.2-q13.31(chr19:11227942-44626354)x3 copy number gain See cases [RCV000133888] Chr19:11227942..44626354 [GRCh38]
Chr19:11338618..45129651 [GRCh37]
Chr19:11199618..49821491 [NCBI36]
Chr19:19p13.2-q13.31		 pathogenic
NR_040109.1(PCAT19):n.1154-2351C>A single nucleotide variant Lung cancer [RCV000101263] Chr19:41458838 [GRCh38]
Chr19:41964744 [GRCh37]
Chr19:19q13.2		 uncertain significance
NR_040109.1(PCAT19):n.469A>G single nucleotide variant Lung cancer [RCV000101264] Chr19:41495020 [GRCh38]
Chr19:42000928 [GRCh37]
Chr19:19q13.2		 uncertain significance
GRCh38/hg38 19q13.12-13.2(chr19:37319377-42738688)x3 copy number gain See cases [RCV000050636] Chr19:37319377..42738688 [GRCh38]
Chr19:37810279..43242840 [GRCh37]
Chr19:42502119..47934680 [NCBI36]
Chr19:19q13.12-13.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1186
Count of miRNA genes:693
Interacting mature miRNAs:793
Transcripts:ENST00000588495, ENST00000594315, ENST00000595063, ENST00000595837, ENST00000597702, ENST00000598215, ENST00000599801
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 190 179 426 5 235 5 732 139 139 51 204 991 1016 158 1
Low 2112 2005 1225 557 332 396 3292 1979 3354 309 1118 401 161 188 2569 1
Below cutoff 94 715 64 55 912 58 222 67 204 49 98 165 7 61 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_040109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_136334 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001756399 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001756400 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_002958911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC005795 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC005945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC011526 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC243960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK309432 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC070102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  OA987039 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  OA987040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  OA987044 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  OA987045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  OA987047 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  OA987048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  OA987049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  OA987050 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000588495
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,164 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000594315
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,455,020 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000595063
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,455,665 - 41,479,141 (-)Ensembl
RefSeq Acc Id: ENST00000595837
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,455,317 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000597702
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,455,257 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000598215
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,456,029 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000599801
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,481 - 41,479,141 (-)Ensembl
RefSeq Acc Id: ENST00000650748
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000650788
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000650804
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,678 (-)Ensembl
RefSeq Acc Id: ENST00000650991
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,493,913 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000651016
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,657 (-)Ensembl
RefSeq Acc Id: ENST00000651156
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000651285
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,457,149 (-)Ensembl
RefSeq Acc Id: ENST00000651291
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,457,386 (-)Ensembl
RefSeq Acc Id: ENST00000651464
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,457,155 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000651572
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,501,255 (-)Ensembl
RefSeq Acc Id: ENST00000651651
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,629 (-)Ensembl
RefSeq Acc Id: ENST00000651712
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,173 - 41,457,299 (-)Ensembl
RefSeq Acc Id: ENST00000651789
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,173 - 41,479,141 (-)Ensembl
RefSeq Acc Id: ENST00000651806
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000651979
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,477,169 - 41,500,641 (-)Ensembl
RefSeq Acc Id: ENST00000652015
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000652127
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,457,280 (-)Ensembl
RefSeq Acc Id: ENST00000652144
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,649 (-)Ensembl
RefSeq Acc Id: ENST00000652160
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,455,713 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000652279
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,173 - 41,457,400 (-)Ensembl
RefSeq Acc Id: ENST00000652333
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,449,520 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000652406
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,657 (-)Ensembl
RefSeq Acc Id: ENST00000652484
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,181 - 41,479,713 (-)Ensembl
RefSeq Acc Id: ENST00000652511
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,457,149 (-)Ensembl
RefSeq Acc Id: ENST00000652558
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000656967
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000664904
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,500,644 (-)Ensembl
RefSeq Acc Id: ENST00000668141
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1941,454,169 - 41,457,282 (-)Ensembl
RefSeq Acc Id: NR_040109
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381941,454,169 - 41,500,649 (-)NCBI
GRCh371941,960,074 - 42,006,554 (-)NCBI
HuRef1938,391,679 - 38,438,155 (-)NCBI
CHM1_11941,959,704 - 42,006,184 (-)NCBI
T2T-CHM13v2.01944,275,440 - 44,321,937 (-)NCBI
Sequence:
RefSeq Acc Id: NR_136334
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381941,454,169 - 41,500,649 (-)NCBI
CHM1_11941,959,704 - 42,006,184 (-)NCBI
T2T-CHM13v2.01944,275,440 - 44,321,937 (-)NCBI
Sequence:
Promoters
RGD ID:15097235
Promoter ID:EPDNEWNC_H2057
Type:initiation region
Name:PCAT19_2
Description:prostate cancer associated transcript 19 [Source:HGNCSymbol;Acc:HGNC:49593]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381941,479,143 - 41,479,203EPDNEWNC
RGD ID:15097234
Promoter ID:EPDNEWNC_H2058
Type:initiation region
Name:PCAT19_1
Description:prostate cancer associated transcript 19 [Source:HGNCSymbol;Acc:HGNC:49593]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381941,500,644 - 41,500,704EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC PCAT19 COSMIC
Ensembl Genes ENSG00000267107 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000588495 ENTREZGENE
  ENST00000652144 ENTREZGENE
GTEx ENSG00000267107 GTEx
HGNC ID HGNC:49593 ENTREZGENE
Human Proteome Map PCAT19 Human Proteome Map
NCBI Gene PCAT19 ENTREZGENE
OMIM 618192 OMIM
RNAcentral URS0000A76AFD RNACentral
  URS0000A776B1 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-22 PCAT19  prostate cancer associated transcript 19    prostate cancer associated transcript 19 (non-protein coding)  Symbol and/or name change 5135510 APPROVED