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PCGEM1 Gene

RNA gene   GIFtS: 26
GCID: GC02P193614

PCGEM1, Prostate-Specific Transcript (Non-Protein Coding)

(Previous name: prostate-specific transcript 1 (non-protein coding))
  See PCGEM1-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 5.2

Aliases
PCGEM1, Prostate-Specific Transcript (Non-Protein Coding)1 2     Prostate-Specific Transcript 1 (Non-Protein Coding)1
Long Intergenic Non-Protein Coding RNA 711     LINC000712
Non-Protein Coding RNA 711     NCRNA000712
Prostate Cancer Associated Transcript 91     PCAT92

External Ids:    HGNC: 301451   Entrez Gene: 640022   Ensembl: ENSG000002274187   OMIM: 6054435   
ORGUL members:    fRNAdb10:FR109430 FR231598      
H-InvDB12:HIT000074407    
NCBI13:AF223389    
NONCODE14:u1058 n424050    
RNAdb15:LIT1562 EVF17789    

Export aliases for PCGEM1 gene to outside databases

Previous GC identifers: GC02U990271 GC02P193322 GC02P185474


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for PCGEM1 Gene:
PCGEM1 (PCGEM1, prostate-specific transcript (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with PCGEM1 include prostate cancer.

Gene Wiki entry for PCGEM1 Gene

fRNAdb sequence ontologies for PCGEM1 - the ORGUL cluster for this gene includes several descriptions:
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NC_018913.2  NT_005403.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the PCGEM1 gene promoter:
         STAT1   LHX3b/Lhx3b   Nkx2-5   CUTL1   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   HNF-1A   HNF-1   LHX3a/Lhx3a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCGEM1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2q32   Ensembl cytogenetic band:  2q32.3   HGNC cytogenetic band: 2q32.3

PCGEM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCGEM1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P193614:  view genomic region     (about GC identifiers)

Start:
193,614,571 bp from pter      End:
193,641,625 bp from pter
Size:
27,055 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for PCGEM1

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
LNCRNA: Long non-coding RNAs

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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  --

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PCGEM1
Interactions:

    Search GeneGlobe Interaction Network for PCGEM1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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Unigene Cluster for PCGEM1:

PCGEM1, prostate-specific transcript (non-protein coding)
Hs.546994
Unigene Representative Sequence: AF223389
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000454040(lincRNA)(uc002ute.3) ENST00000606314(lincRNA)
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Additional mRNA sequence: 

AF223389.1 NR_002769.1 

1 DOTS entry:

DT.91827634 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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Expression evidence for PCGEM1:RNAdb

PCGEM1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
PCGEM1 Expression
About this image

PCGEM1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.546994
    Custom PCR Arrays for PCGEM1
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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  --

ENSEMBL Gene Tree for PCGEM1 (if available)
TreeFam Gene Tree for PCGEM1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for PCGEM1 (see all 524)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1157488381,2
C,F--193612598(+) CAAGTA/GTCTGA 1 -- us2k11Minor allele frequency- G:0.02WA 118
rs1161399761,2
C,F--193612882(+) CTGCAA/GTTTCT 1 -- us2k11Minor allele frequency- G:0.02WA 118
rs101791241,2
C,F,A,H--193612994(+) TTTGTG/TTTTTT 1 -- us2k14Minor allele frequency- T:0.01NS EA 412
rs1151215161,2
F--193613064(+) GCATAT/AGTTTC 1 -- us2k11Minor allele frequency- A:0.03WA 118
rs13479321,2
F,H--193613071(-) ATACAT/CGGAAA 1 -- us2k15Minor allele frequency- C:0.02NS EA WA 538
rs1399683711,2
--193613179(+) TTTAAA/TAACTA 1 -- us2k10--------
rs1418910061,2
--193613545(+) TGTATA/GCTTTT 1 -- us2k10--------
rs1887546551,2
C--193613671(+) TATACC/TTATTT 1 -- us2k10--------
rs1180562931,2
F--193613743(+) GATCGA/TACAAT 1 -- us2k11Minor allele frequency- T:0.04EA 120
rs101821791,2
C,F,H--193613895(+) TTTTCC/ATATTG 1 -- us2k15Minor allele frequency- A:0.02NS EA WA 538

HapMap Linkage Disequilibrium report for PCGEM1 (193614571 - 193641625 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for PCGEM1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv875633CNV Loss21882294
nsv527665CNV Loss19592680

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing PCGEM1
DNA2.0 Custom Variant and Variant Library Synthesis for PCGEM1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 605443OMIM information: 186973    
1 disease for PCGEM1:    
About MalaCards
prostate cancer


Find genes that share disorders with PCGEM1           About GenesLikeMe

Genetic Association Database (GAD): PCGEM1
Human Genome Epidemiology (HuGE) Navigator: PCGEM1 (1 document)

Export disorders for PCGEM1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for PCGEM1 gene, integrated from 10 sources (see all 15):
(articles sorted by number of sources associating them with PCGEM1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer. (PubMed id 11050243)1, 3, 9 Srikantan V....Srivastava S. (Proc. Natl. Acad. Sci. U.S.A. 2000)
  2. Regulation of apoptosis by a prostate-specific and prostate cancer-associated noncoding gene, PCGEM1. (PubMed id 16569192)1, 3, 9 Fu X....Srivastava S. (DNA Cell Biol. 2006)
  3. Association between lncrna PCGEM1 polymorphisms and prostate cancer risk. (PubMed id 23459097)1, 3 Xue Y....Wu D. (Prostate Cancer Prostatic Dis. 2013)
  4. Risk of breast and prostate cancer is not associated with increased homozygosity in outbred populations. (PubMed id 20407466)1, 4 Enciso-Mora V....Houlston R.S. (Eur. J. Hum. Genet. 2010)
  5. Elevated expression of PCGEM1, a prostate-specific gene with cell growth-promoting function, is associated with high-risk prostate cancer patients. (PubMed id 14724589)1, 9 Petrovics G....Srivastava S. (Oncogene 2004)
  6. lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs. (PubMed id 23945587)1 Yang L....Rosenfeld M.G. (Nature 2013)
  7. Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis. (PubMed id 23453885)1 (Lancet 2013)
  8. Genome-wide association study identifies five new schizophrenia loci. (PubMed id 21926974)1 (Nat. Genet. 2011)
  9. Differential effects of cholesterol and phytosterols on cell proliferation, apoptosis and expression of a prostate specific gene in prostate cancer cell lines. (PubMed id 19186008)1 Ifere G.O....Ananaba G.A. (Cancer Detect. Prev. 2009)
  10. Prostate cancer gene expression marker 1 (PCGEM1): a patented prostate- specific non-coding gene and regulator of prostate cancer progression. (PubMed id 19891595)9 Ifere G.O. and Ananaba G.A. (amp 2009)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 64002 HGNC: 30145 Ensembl:ENSG00000227418 euGenes: HUgn64002 ECgene: PCGEM1
H-InvDB: PCGEM1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for PCGEM1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for PCGEM1 gene:
Search GeneIP for patents involving PCGEM1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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