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PDZK1P1 Gene

pseudogene   GIFtS: 20
GCID: GC01M145924

PDZ Domain Containing 1 Pseudogene 1

  Search for PDZK1P1
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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Aliases
PDZ Domain Containing 1 Pseudogene 11 2

External Ids:    HGNC: 319741   Entrez Gene: 7289392   Ensembl: ENSG000002158607   UniProtKB: A8MUH73   

Export aliases for PDZK1P1 gene to outside databases

Previous GC identifer: GC01M144634


(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 PDZK1P1 Gene:
PDZK1P1 (PDZ domain containing 1 pseudogene 1) is a pseudogene.


(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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Regulatory elements:
   Regulatory transcription factor binding sites in the PDZK1P1 gene promoter:
         ISGF-3   Ik-2   HNF-1   CUTL1   HNF-1A   Ik-1   
         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 PDZK1P1


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

Entrez Gene cytogenetic band: 1q21.1   Ensembl cytogenetic band:  1q21.1   HGNC cytogenetic band: 1q21.1

PDZK1P1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PDZK1P1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M145924:  view genomic region     (about GC identifiers)

Start:
145,924,388 bp from pter      End:
145,942,619 bp from pter
Size:
18,232 bases      Orientation:
minus strand

(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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: PDZ1P_HUMAN, A8MUH7 (See protein sequence)
Recommended Name: Putative PDZ domain-containing protein 1P  
Size: 402 amino acids; 44056 Da
Caution: Could be the product of a pseudogene
Alternative splicing: 2 isoforms:  A8MUH7-1   A8MUH7-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PDZK1P1: NX_A8MUH7

Explore proteomics data for PDZK1P1 at MOPED


See PDZK1P1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR001478 PDZ

Graphical View of Domain Structure for InterPro Entry A8MUH7

ProtoNet protein and cluster: A8MUH7

UniProtKB/Swiss-Prot: PDZ1P_HUMAN, A8MUH7
Similarity: Belongs to the NHER family
Similarity: Contains 3 PDZ (DHR) domains


PDZK1P1 for domains           About GeneDecksing


(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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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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 PDZK1P1
Interactions:

    Search GeneGlobe Interaction Network for PDZK1P1

(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 Tocris compounds for PDZK1P1 (PDZ1P)



(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, Primers from OriGene, and/or QIAGEN )
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2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000401011(uc010ozf.2 uc001eov.1) ENST00000449151
miRNA
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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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PDZK1P1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
PDZK1P1 Expression
About this image


PDZK1P1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 
 NULL (Uncategorized)
         Definitive endoderm-like cells
PDZK1P1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

PDZK1P1 Protein Expression
    Custom PCR Arrays for PDZK1P1
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PDZK1P1

(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 PDZK1P1 (if available)
TreeFam Gene Tree for PDZK1P1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for PDZK1P1 gene
7 SIMAP similar genes for PDZK1P1 using alignment to 1 protein entry:     PDZ1P_HUMAN:
PDZK1    TJP2    DLG4    ARHGAP23    PDZD3    SLC9A3R1
SLC9A3R2

PDZK1P1 for paralogs           About GeneDecksing



(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 PDZK1P1 (see all 43)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs2022456771,2
C--145931852(+) TCTGTA/CCATGT 1 -- nc-transcript-variant0--------
rs1834080291,2
--145942767(+) TTTGAA/GCATTC 1 -- us2k10--------
rs1452388411,2
C--145942819(+) GGAGTA/GGGAGT 1 -- us2k10--------
rs2010265291,2
C--145942825(+) GGAGTC/GCTGAT 1 -- us2k10--------
rs1996075781,2
C--145942850(+) ATCATA/GGATTA 1 -- us2k10--------
rs2002954741,2
C--145942899(+) TCCCCA/GGATTT 1 -- us2k10--------
rs23065241,2
C,F--154468940(-) GAAAAT/CGACAA 1 -- int14Minor allele frequency- C:0.40EA NA 1226
rs563276541,2
C--154475760(+) ACCATA/GATACC 1 -- int10--------
rs26247051,2
A--154482155(-) GGAAGC/TACCAG 1 -- int10--------
rs27991121,2
A--154482217(+) GATGCA/GCCTCA 1 -- int10--------

HapMap Linkage Disequilibrium report for PDZK1P1 (145924388 - 145942619 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for PDZK1P1 (see all 11):    About this table    
Variant IDTypeSubtypePubMed ID
dgv15n16CNV Deletion17901297
dgv46e201CNV Deletion23290073
nsv8180CNV Loss18304495
nsv511130CNV Loss21212237
nsv8114CNV Loss18304495
nsv428224CNV Gain18775914
nsv872268CNV Gain21882294
esv529CNV CNV17122850
dgv113e1CNV Complex17122850
dgv114e1CNV Complex17122850

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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(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 PDZK1P1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with PDZK1P1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  2. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)

(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: 728939 HGNC: 31974 Ensembl:ENSG00000215860 euGenes: HUgn728939 ECgene: PDZK1P1
H-InvDB: PDZK1P1

(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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(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for PDZK1P1 gene:
Search GeneIP for patents involving PDZK1P1

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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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