PCAT18 (prostate cancer associated transcript 18) - Rat Genome Database

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Gene: PCAT18 (prostate cancer associated transcript 18) Homo sapiens
Analyze
Symbol: PCAT18
Name: prostate cancer associated transcript 18
RGD ID: 7849120
HGNC Page HGNC:49211
Description: Predicted to be involved in RNA processing. Predicted to be located in nucleolus.
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LINC01092; prostate cancer associated transcript 18 (non-protein coding)
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381826,687,621 - 26,703,638 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1826,658,954 - 26,703,783 (-)EnsemblGRCh38hg38GRCh38
GRCh371824,267,585 - 24,283,602 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361822,523,356 - 22,537,600 (-)NCBINCBI36Build 36hg18NCBI36
Celera1821,078,200 - 21,094,222 (-)NCBICelera
Cytogenetic Map18q11.2NCBI
HuRef1821,117,315 - 21,133,334 (-)NCBIHuRef
CHM1_11824,195,044 - 24,211,057 (-)NCBICHM1_1
T2T-CHM13v2.01826,881,680 - 26,897,703 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component
nucleolus  (IEA)

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11181995   PMID:14702039   PMID:24519926   PMID:30518158   PMID:32119960   PMID:33006448   PMID:34787047  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 18p11.32-q23(chr18:149089-80234391)x3 copy number gain See cases [RCV000134110] Chr18:149089..80234391 [GRCh38]
Chr18:149089..77992274 [GRCh37]
Chr18:139089..76093265 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:118760-80254946)x3 copy number gain See cases [RCV000138656] Chr18:118760..80254946 [GRCh38]
Chr18:118760..78012829 [GRCh37]
Chr18:108760..76113817 [NCBI36]
Chr18:18p11.32-q23		 pathogenic|conflicting data from submitters
GRCh38/hg38 18p11.32-q23(chr18:149089-80254936)x3 copy number gain See cases [RCV000139397] Chr18:149089..80254936 [GRCh38]
Chr18:149089..78012819 [GRCh37]
Chr18:139089..76113807 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q11.1-12.1(chr18:20949378-34363455)x3 copy number gain See cases [RCV000141646] Chr18:20949378..34363455 [GRCh38]
Chr18:18529339..31943419 [GRCh37]
Chr18:16783337..30197417 [NCBI36]
Chr18:18q11.1-12.1		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:136227-80256240)x3 copy number gain See cases [RCV000142244] Chr18:136227..80256240 [GRCh38]
Chr18:136227..78014123 [GRCh37]
Chr18:126227..76115097 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q11.1-12.3(chr18:20941324-40360620)x3 copy number gain See cases [RCV000142226] Chr18:20941324..40360620 [GRCh38]
Chr18:18521285..37940584 [GRCh37]
Chr18:16775283..36194582 [NCBI36]
Chr18:18q11.1-12.3		 pathogenic
GRCh38/hg38 18q11.1-22.3(chr18:20962119-74691446)x3 copy number gain See cases [RCV000143057] Chr18:20962119..74691446 [GRCh38]
Chr18:18542080..72403402 [GRCh37]
Chr18:16796078..70532390 [NCBI36]
Chr18:18q11.1-22.3		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:136226-80256240)x3 copy number gain See cases [RCV000143218] Chr18:136226..80256240 [GRCh38]
Chr18:136226..78014123 [GRCh37]
Chr18:126226..76115097 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148963-80252149)x3 copy number gain See cases [RCV000148072] Chr18:148963..80252149 [GRCh38]
Chr18:148963..78010032 [GRCh37]
Chr18:138963..76111023 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:53345-80209986)x3 copy number gain See cases [RCV000052501] Chr18:53345..80209986 [GRCh38]
Chr18:53345..77967869 [GRCh37]
Chr18:43345..76068860 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148763-80252290)x3 copy number gain See cases [RCV000052507] Chr18:148763..80252290 [GRCh38]
Chr18:148763..78010173 [GRCh37]
Chr18:138763..76111164 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148963-80244381)x3 copy number gain See cases [RCV000052514] Chr18:148963..80244381 [GRCh38]
Chr18:148963..78002264 [GRCh37]
Chr18:138963..76103255 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q11.1-23(chr18:20960320-80234429)x3 copy number gain See cases [RCV000052543] Chr18:20960320..80234429 [GRCh38]
Chr18:18540281..77992312 [GRCh37]
Chr18:16794279..76093303 [NCBI36]
Chr18:18q11.1-23		 pathogenic
GRCh38/hg38 18q11.1-12.1(chr18:20960320-28601877)x3 copy number gain See cases [RCV000052545] Chr18:20960320..28601877 [GRCh38]
Chr18:18540281..26181841 [GRCh37]
Chr18:16794279..24435839 [NCBI36]
Chr18:18q11.1-12.1		 pathogenic
GRCh38/hg38 18q11.1-23(chr18:20989762-80209986)x3 copy number gain See cases [RCV000052549] Chr18:20989762..80209986 [GRCh38]
Chr18:18569723..77967869 [GRCh37]
Chr18:16823721..76068860 [NCBI36]
Chr18:18q11.1-23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148963-80252149)x3 copy number gain See cases [RCV000051048] Chr18:148963..80252149 [GRCh38]
Chr18:148963..78010032 [GRCh37]
Chr18:138963..76111023 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:83
Count of miRNA genes:83
Interacting mature miRNAs:83
Transcripts:ENST00000579458
Prediction methods: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

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
479 1998 1499 830 4682 1616 1971 3 520 921 368 1736 3815 3091 51 3553 731 1544 1338 164

Sequence


Ensembl Acc Id: ENST00000579458
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1826,687,621 - 26,703,783 (-)Ensembl
Ensembl Acc Id: ENST00000830732
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1826,658,954 - 26,703,685 (-)Ensembl
Ensembl Acc Id: ENST00000830733
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1826,666,394 - 26,703,687 (-)Ensembl
Ensembl Acc Id: ENST00000830734
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1826,667,106 - 26,703,687 (-)Ensembl
Ensembl Acc Id: ENST00000830735
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1826,694,899 - 26,703,639 (-)Ensembl
RefSeq Acc Id: NR_024259
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381826,687,621 - 26,703,638 (-)NCBI
GRCh371824,267,585 - 24,283,602 (-)NCBI
HuRef1821,117,315 - 21,133,334 (-)NCBI
CHM1_11824,195,044 - 24,211,057 (-)NCBI
T2T-CHM13v2.01826,881,680 - 26,897,703 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein EAX01221 (Get FASTA)   NCBI Sequence Viewer  

Promoters
RGD ID:15097147
Promoter ID:EPDNEWNC_H1975
Type:initiation region
Name:PCAT18_1
Description:prostate cancer associated transcript 18 [Source:HGNCSymbol;Acc:HGNC:49211]
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
GRCh381826,703,638 - 26,703,698EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC PCAT18 COSMIC
Ensembl Genes ENSG00000265369 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000579458 ENTREZGENE
GTEx ENSG00000265369 GTEx
HGNC ID HGNC:49211 ENTREZGENE
Human Proteome Map PCAT18 Human Proteome Map
NCBI Gene PCAT18 ENTREZGENE
OMIM 617647 OMIM
RNAcentral URS000016073B RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-22 PCAT18  prostate cancer associated transcript 18    prostate cancer associated transcript 18 (non-protein coding)  Symbol and/or name change 5135510 APPROVED