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PART1 Gene

RNA gene   GIFtS: 33
GCID: GC05P059797

Prostate Androgen-Regulated Transcript 1 (Non-Protein Coding)

  See PART1-related diseases
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): antisense

Quality score for this RNA gene is 3

Aliases
Prostate Androgen-Regulated Transcript 1 (Non-Protein Coding)1 2
Non-Protein Coding RNA 2061
NCRNA002062

External Ids:    HGNC: 172631   Entrez Gene: 258592   Ensembl: ENSG000001529317   OMIM: 6049915   
ORGUL members:         

Export aliases for PART1 gene to outside databases

Previous GC identifers: GC05P059935 GC05P061321 GC05P059754 GC05P059799 GC05P059819 GC05P056741


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PART1 Gene:
This gene is induced by androgen in prostate adenocarcinoma cells. Multiple alternatively transcript variants have
been described for this gene, none of which are predicted to encode a protein product. (provided by RefSeq, Sep
2009)

GeneCards Summary for PART1 Gene:
PART1 (prostate androgen-regulated transcript 1 (non-protein coding)) is an RNA gene, and is affiliated with the antisense RNA class. Diseases associated with PART1 include prostate adenocarcinoma, and adenocarcinoma.




(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_000005.9  NC_018916.2  NT_034772.7  
Regulatory elements:
   Regulatory transcription factor binding sites in the PART1 gene promoter:
         Pbx1a   HSF1 (long)   C/EBPalpha   S8   POU2F1   POU2F1a   FOXJ2 (long isoform)   HSF1short   ARP-1   FOXJ2   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PART1


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

Entrez Gene cytogenetic band: 5q12.1   Ensembl cytogenetic band:  5q12.1   HGNC cytogenetic band: 5q12.1

PART1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PART1 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P059797:  view genomic region     (about GC identifiers)

Start:
59,783,540 bp from pter      End:
59,843,484 bp from pter
Size:
59,945 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for PART1

(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, 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, 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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Phenotypes:
     2 GenomeRNAi human phenotypes for PART1:
 Decreased influenza A/WSN/33 r  Increased gamma-H2AX phosphory 

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for PART1

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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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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol2
extracellular2
nucleus2
plasma membrane1

(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 PART1
Interactions:

    Search GeneGlobe Interaction Network for PART1

(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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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for PART1



(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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REFSEQ mRNAs for PART1 gene (2 alternative transcripts): 
NM_001039499.1  NM_001040639.1  

Unigene Cluster for PART1:

Prostate androgen-regulated transcript 1 (non-protein coding)
Hs.146312  [show with all ESTs]
Unigene Representative Sequence: NR_028509
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000515734(lincRNA)(uc003jsf.4 uc021xza.1) ENST00000506884(lincRNA)(uc003jsg.2)
ENST00000504876(lincRNA)
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Additional mRNA sequence: 

AF070547.1 AK094518.1 AK095768.1 AK312071.1 AL050198.1 BC069304.1 BC096696.1 BC096727.1 
BC098111.1 NR_024617.1 NR_028508.1 NR_028509.1 

8 DOTS entries:

DT.310355  DT.99933158  DT.100016276  DT.120842783  DT.120842529  DT.91755706  DT.40291987  DT.95192816 

Selected AceView cDNA sequences (see all 51):

BX093743 AF163475 AK094518 NM_016590 AA410580 AI739050 AI759995 AW139625 
AA419011 AI269149 AW135514 BC069304 BI752189 BQ898163 AI627693 AI970017 
BP346540 BV199297 AI870129 BI913968 BM126341 AA411616 BF594842 AI761105 

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 PART1:none

PART1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AAATGCAGGA
PART1 Expression
About this image

PART1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.146312
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In Situ
Assay Products:
 

 
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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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This gene was present in the common ancestor of human and mouse.

Orthologs for PART1 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia UN5 prostate androgen-regulated transcript 1   --   N/A -


ENSEMBL Gene Tree for PART1 (if available)
TreeFam Gene Tree for PART1 (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 PART1 (see all 1005)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 5 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1854211891,2
--59786165(+) ATAGCA/GGGGGC 3 -- int1 nc-transcript-variant0--------
rs1153845621,2
C,F--59786261(+) AGCCTG/ATGCAA 3 -- int1 nc-transcript-variant1Minor allele frequency- A:0.04WA 118
rs743650041,2
C,F--59786358(+) GTCTGC/TTTCCT 3 -- int1 nc-transcript-variant2Minor allele frequency- T:0.05CSA WA 120
rs1886991311,2
--59786391(+) CAGGAC/TTTGTA 3 -- int1 nc-transcript-variant0--------
rs1919778321,2
C--59786633(+) TGTCAG/TCAAAT 3 -- int1 nc-transcript-variant0--------
rs1845338291,2
--59786771(+) AGTAAA/CCTATA 3 -- int1 nc-transcript-variant0--------
rs1888427521,2
--59786802(+) TGTTAA/GTATGT 3 -- int1 nc-transcript-variant0--------
rs1917334561,2
--59786833(+) GGGTAC/TTAACT 3 -- int1 nc-transcript-variant0--------
rs1845827981,2
--59787020(+) AATGTC/TAGCAA 3 -- int1 nc-transcript-variant0--------
rs2014337461,2
C--59787051(+) AAAAA-/ATGCTT 3 -- int1 nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for PART1 (59783540 - 59843484 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for PART1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv327281CNV Loss16902084
nsv881711CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
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(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: 604991    OMIM disorders: --

2 diseases for PART1:    
About MalaCards
prostate adenocarcinoma    adenocarcinoma

1 disease from the University of Copenhagen DISEASES database for PART1:
Syphilis

Find genes that share disorders with PART1           About GenesLikeMe

Genetic Association Database (GAD): PART1

Export disorders for PART1 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 PART1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with PART1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. PART-1: a novel human prostate-specific, androgen-regulated gene that maps to chromosome 5q12. (PubMed id 10706094)1, 3, 9 Lin B....Nelson P.S. (Cancer Res. 2000)
  2. A long non-coding RNA signature in glioblastoma multiforme predicts survival. (PubMed id 23726844)1, 3 Zhang X.Q....Leung G.K. (Neurobiol. Dis. 2013)
  3. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (BMC Med. Genet. 2007)
  4. Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study. (PubMed id 17903301)4 Vasan R.S....Benjamin E.J. (BMC Med. Genet. 2007)
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1 Gerhard D.S.... Malek J. (Genome Res. 2004)
  6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  8. Large-scale concatenation cDNA sequencing. (PubMed id 9110174)1 Yu W.... Gibbs R.A. (Genome Res. 1997)
  9. A "double adaptor" method for improved shotgun library construction. (PubMed id 8619474)1 Andersson B.... Gibbs R.A. (Anal. Biochem. 1996)
  10. Genistein and daidzein downregulate prostate androgen-regulated transcript-1 (PART-1) gene expression induced by dihydrotestosterone in human prostate LNCaP cancer cells. (PubMed id 12566472)9 Yu L....Zhou J.R. (J. Nutr. 2003)

(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: 25859 HGNC: 17263 AceView: PART1 Ensembl:ENSG00000152931 euGenes: HUgn25859
ECgene: PART1 H-InvDB: PART1

(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 PART1 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 PART1 gene:
Search GeneIP for patents involving PART1

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



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Advanced Cell Diagnostics, Animal models from genOway)
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