PCAT6 (prostate cancer associated transcript 6) - Rat Genome Database

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Gene: PCAT6 (prostate cancer associated transcript 6) Homo sapiens
Analyze
Symbol: PCAT6
Name: prostate cancer associated transcript 6
RGD ID: 5687782
HGNC Page HGNC:43714
Description: ASSOCIATED WITH familial adult myoclonic epilepsy 5; Gastrointestinal stroma tumor; gastrointestinal stromal tumor; INTERACTS WITH acrylamide; cadmium dichloride; fipronil
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: KDM5B-AS1; KDM5BAS1; ncRNA-a2; onco-lncRNA-96; PCAN-R1; prostate cancer associated transcript 6 (non-protein coding)
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381202,810,946 - 202,811,913 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1202,810,850 - 202,812,473 (+)EnsemblGRCh38hg38GRCh38
GRCh371202,780,074 - 202,781,041 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera1175,909,294 - 175,910,260 (+)NCBICelera
Cytogenetic Map1q32.1NCBI
HuRef1173,945,661 - 173,946,628 (+)NCBIHuRef
CHM1_11204,202,313 - 204,203,280 (+)NCBICHM1_1
T2T-CHM13v2.01202,073,605 - 202,074,572 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Human Phenotype
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:20887892   PMID:23728290   PMID:25864709   PMID:27458097   PMID:30314898   PMID:30569799   PMID:30915737   PMID:30938104   PMID:31646553   PMID:31676070   PMID:32039820   PMID:32064636  
PMID:32339330   PMID:32908134   PMID:32990800   PMID:33090394   PMID:33125146   PMID:33142195   PMID:33761616   PMID:34185427   PMID:35081872   PMID:35609331   PMID:36787056   PMID:36949349  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q31.1-42.11(chr1:187143981-224299417)x3 copy number gain See cases [RCV000051857] Chr1:187143981..224299417 [GRCh38]
Chr1:187113113..224487119 [GRCh37]
Chr1:185379736..222553742 [NCBI36]
Chr1:1q31.1-42.11		 pathogenic
GRCh38/hg38 1q32.1(chr1:200144603-203112078)x1 copy number loss See cases [RCV000133625] Chr1:200144603..203112078 [GRCh38]
Chr1:200113731..203081206 [GRCh37]
Chr1:198380354..201347829 [NCBI36]
Chr1:1q32.1		 pathogenic
GRCh37/hg19 1q31.3-42.13(chr1:197811907-228997888)x3 copy number gain See cases [RCV000240137] Chr1:197811907..228997888 [GRCh37]
Chr1:1q31.3-42.13		 pathogenic
GRCh37/hg19 1q31.3-44(chr1:195483439-249213000)x3 copy number gain See cases [RCV000449172] Chr1:195483439..249213000 [GRCh37]
Chr1:1q31.3-44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1q32.1(chr1:202604386-202912995)x3 copy number gain not provided [RCV000736832] Chr1:202604386..202912995 [GRCh37]
Chr1:1q32.1		 benign
GRCh37/hg19 1q32.1(chr1:202765279-202847719)x1 copy number loss not provided [RCV000736833] Chr1:202765279..202847719 [GRCh37]
Chr1:1q32.1		 benign
GRCh37/hg19 1q25.3-41(chr1:185644663-221698833)x3 copy number gain not provided [RCV000749265] Chr1:185644663..221698833 [GRCh37]
Chr1:1q25.3-41		 pathogenic
GRCh37/hg19 1q32.1(chr1:202542202-203108963)x3 copy number gain not provided [RCV000749330] Chr1:202542202..203108963 [GRCh37]
Chr1:1q32.1		 benign
GRCh37/hg19 1q25.3-44(chr1:182388773-249111240)x3 copy number gain not provided [RCV000845852] Chr1:182388773..249111240 [GRCh37]
Chr1:1q25.3-44		 pathogenic
GRCh37/hg19 1q32.1(chr1:202575619-202880256)x3 copy number gain not provided [RCV000848091] Chr1:202575619..202880256 [GRCh37]
Chr1:1q32.1		 uncertain significance
GRCh37/hg19 1q31.3-32.2(chr1:194356425-210988710)x3 copy number gain not provided [RCV001249273] Chr1:194356425..210988710 [GRCh37]
Chr1:1q31.3-32.2		 not provided
NC_000001.10:g.(?_130980840)_(248900000_?)dup duplication Gastrointestinal stromal tumor [RCV001300221]|Parathyroid carcinoma [RCV001341077] Chr1:130980840..248900000 [GRCh37]
Chr1:1q12-44		 uncertain significance
GRCh37/hg19 1q32.1(chr1:202638835-202876250)x3 copy number gain not provided [RCV001827631] Chr1:202638835..202876250 [GRCh37]
Chr1:1q32.1		 uncertain significance
NC_000001.10:g.(?_200522516)_(206945780_?)dup duplication Epilepsy, familial adult myoclonic, 5 [RCV003116306] Chr1:200522516..206945780 [GRCh37]
Chr1:1q32.1		 uncertain significance
NC_000001.10:g.(?_200522516)_(208391267_?)dup duplication Hypokalemic periodic paralysis, type 1 [RCV003119239]|not provided [RCV003119240] Chr1:200522516..208391267 [GRCh37]
Chr1:1q32.1-32.2		 uncertain significance|no classifications from unflagged records
GRCh37/hg19 1q31.3-44(chr1:197867914-249224684)x3 copy number gain See cases [RCV002287837] Chr1:197867914..249224684 [GRCh37]
Chr1:1q31.3-44		 pathogenic
GRCh37/hg19 1q25.3-32.3(chr1:181453460-213107248)x3 copy number gain not provided [RCV002475637] Chr1:181453460..213107248 [GRCh37]
Chr1:1q25.3-32.3		 pathogenic
GRCh37/hg19 1q32.1(chr1:202618779-202889022)x3 copy number gain not provided [RCV003484049] Chr1:202618779..202889022 [GRCh37]
Chr1:1q32.1		 uncertain significance
GRCh37/hg19 1q31.3-32.1(chr1:197216705-203683110)x1 copy number loss not specified [RCV003986384] Chr1:197216705..203683110 [GRCh37]
Chr1:1q31.3-32.1		 likely pathogenic
GRCh37/hg19 1q32.1(chr1:199373229-204335027)x3 copy number gain not specified [RCV003986684] Chr1:199373229..204335027 [GRCh37]
Chr1:1q32.1		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:771
Count of miRNA genes:395
Interacting mature miRNAs:423
Transcripts:ENST00000417262, ENST00000425295, ENST00000553157
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
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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 29 4 254 35 32 20 1382 11 261 64 644 137 17 9 630 2
Low 2390 2285 1416 535 1278 390 2885 2042 3458 351 810 1463 156 1 1190 2069 3 2
Below cutoff 17 648 56 54 547 55 88 140 14 4 5 9 1 5 88 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000417262
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,962 - 202,811,913 (+)Ensembl
RefSeq Acc Id: ENST00000425295
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,883 - 202,811,915 (+)Ensembl
RefSeq Acc Id: ENST00000553157
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,954 - 202,812,156 (+)Ensembl
RefSeq Acc Id: ENST00000660963
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,954 - 202,811,912 (+)Ensembl
RefSeq Acc Id: ENST00000685610
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,926 - 202,811,912 (+)Ensembl
RefSeq Acc Id: ENST00000685748
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,850 - 202,811,915 (+)Ensembl
RefSeq Acc Id: ENST00000686658
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,850 - 202,812,473 (+)Ensembl
RefSeq Acc Id: ENST00000687305
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,883 - 202,812,473 (+)Ensembl
RefSeq Acc Id: ENST00000688063
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,935 - 202,811,915 (+)Ensembl
RefSeq Acc Id: ENST00000690240
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,876 - 202,811,915 (+)Ensembl
RefSeq Acc Id: ENST00000690767
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,896 - 202,811,913 (+)Ensembl
RefSeq Acc Id: ENST00000691356
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,921 - 202,811,912 (+)Ensembl
RefSeq Acc Id: ENST00000692796
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,896 - 202,811,913 (+)Ensembl
RefSeq Acc Id: ENST00000692814
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,926 - 202,811,912 (+)Ensembl
RefSeq Acc Id: ENST00000692992
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,911 - 202,811,913 (+)Ensembl
RefSeq Acc Id: ENST00000693272
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1202,810,921 - 202,811,912 (+)Ensembl
RefSeq Acc Id: NR_046325
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381202,810,946 - 202,811,913 (+)NCBI
HuRef1173,945,661 - 173,946,628 (+)NCBI
CHM1_11204,202,313 - 204,203,280 (+)NCBI
T2T-CHM13v2.01202,073,605 - 202,074,572 (+)NCBI
Sequence:
RefSeq Acc Id: NR_046326
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381202,810,946 - 202,811,913 (+)NCBI
HuRef1173,945,661 - 173,946,628 (+)NCBI
CHM1_11204,202,313 - 204,203,280 (+)NCBI
T2T-CHM13v2.01202,073,605 - 202,074,572 (+)NCBI
Sequence:
Promoters
RGD ID:15095330
Promoter ID:EPDNEWNC_H165
Type:initiation region
Name:PCAT6_1
Description:prostate cancer associated transcript 6 [Source:HGNCSymbol;Acc:HGNC:43714]
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
GRCh381202,810,955 - 202,811,015EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC PCAT6 COSMIC
Ensembl Genes ENSG00000228288 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000417262 ENTREZGENE
  ENST00000425295 ENTREZGENE
GTEx ENSG00000228288 GTEx
HGNC ID HGNC:43714 ENTREZGENE
Human Proteome Map PCAT6 Human Proteome Map
NCBI Gene KDM5B-AS1 ENTREZGENE
RNAcentral URS000075BE9F RNACentral
  URS000075CFCD RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-22 PCAT6  prostate cancer associated transcript 6    prostate cancer associated transcript 6 (non-protein coding)  Symbol and/or name change 5135510 APPROVED
2013-06-18 PCAT6  prostate cancer associated transcript 6 (non-protein coding)  KDM5B-AS1  KDM5B antisense RNA 1 (head to head)  Symbol and/or name change 5135510 APPROVED
2012-10-23 KDM5B-AS1  KDM5B antisense RNA 1 (head to head)    KDM5B antisense RNA 1  Symbol and/or name change 5135510 APPROVED
2012-08-21 KDM5B-AS1  KDM5B antisense RNA 1  KDM5B-AS1  KDM5B antisense RNA 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED