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PDZD2 PDZ domain containing 2 [ Homo sapiens (human) ]

Gene ID: 23037, updated on 5-Aug-2018

Summary

Official Symbol
PDZD2provided by HGNC
Official Full Name
PDZ domain containing 2provided by HGNC
Primary source
HGNC:HGNC:18486
See related
Ensembl:ENSG00000133401 MIM:610697; Vega:OTTHUMG00000161981
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AIPC; PIN1; PAPIN; PDZK3
Summary
The protein encoded by this gene contains six PDZ domains and shares sequence similarity with pro-interleukin-16 (pro-IL-16). Like pro-IL-16, the encoded protein localizes to the endoplasmic reticulum and is thought to be cleaved by a caspase to produce a secreted peptide containing two PDZ domains. In addition, this gene is upregulated in primary prostate tumors and may be involved in the early stages of prostate tumorigenesis. [provided by RefSeq, Dec 2015]
Expression
Biased expression in fat (RPKM 15.3), ovary (RPKM 9.0) and 12 other tissues See more
Orthologs

Genomic context

See PDZD2 in Genome Data Viewer
Location:
5p13.3
Exon count:
30
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (31639388..32110932)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (31639345..32111038)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene chromosome 5 open reading frame 22 Neighboring gene RNA, U6 small nuclear 363, pseudogene Neighboring gene RNA, U6 small nuclear 358, pseudogene Neighboring gene RNA, U6 small nuclear 760, pseudogene Neighboring gene ribosomal protein L9 pseudogene 17 Neighboring gene ribosomal protein L21 pseudogene 56 Neighboring gene ribosomal protein L5 pseudogene 14 Neighboring gene mitochondrial import receptor subunit TOM7 homolog pseudogene Neighboring gene tumor protein, translationally-controlled 1 pseudogene 5 Neighboring gene microRNA 4279 Neighboring gene uncharacterized LOC105374711 Neighboring gene golgi phosphoprotein 3 Neighboring gene ribosomal protein L27 pseudogene 10

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Citalopram and escitalopram plasma drug and metabolite concentrations: genome-wide associations.
NHGRI GWA Catalog
Common variation at 2q22.3 (ZEB2) influences the risk of renal cancer.
NHGRI GWA Catalog
Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0300

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell-cell junction ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
extracellular region ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 

General protein information

Preferred Names
PDZ domain-containing protein 2
Names
PDZ domain-containing protein 3
activated in prostate cancer protein
plakophilin-related armadillo repeat protein-interactive PDZ protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033962.2 RefSeqGene

    Range
    5001..476523
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_178140.3NP_835260.2  PDZ domain-containing protein 2

    See identical proteins and their annotated locations for NP_835260.2

    Status: REVIEWED

    Source sequence(s)
    AB002298, AC025178, CA503068
    Consensus CDS
    CCDS34137.1
    UniProtKB/Swiss-Prot
    O15018
    UniProtKB/TrEMBL
    A0A024RE15
    Related
    ENSP00000402033.1, OTTHUMP00000220935, ENST00000438447.1, OTTHUMT00000366608
    Conserved Domains (2) summary
    smart00228
    Location:27512833
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:589670
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    31639388..32110932
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005248269.4XP_005248326.1  PDZ domain-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_005248326.1

    Conserved Domains (2) summary
    smart00228
    Location:27852867
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:589670
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  2. XM_011513994.2XP_011512296.1  PDZ domain-containing protein 2 isoform X2

    Conserved Domains (2) summary
    smart00228
    Location:27732855
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:589670
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  3. XM_011513992.2XP_011512294.1  PDZ domain-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011512294.1

    Conserved Domains (2) summary
    smart00228
    Location:27852867
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:589670
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  4. XM_011513996.2XP_011512298.1  PDZ domain-containing protein 2 isoform X4

    Conserved Domains (2) summary
    smart00228
    Location:26932775
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:497578
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  5. XM_011513993.2XP_011512295.1  PDZ domain-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011512295.1

    Conserved Domains (2) summary
    smart00228
    Location:27852867
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:589670
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  6. XM_011513995.2XP_011512297.1  PDZ domain-containing protein 2 isoform X3

    See identical proteins and their annotated locations for XP_011512297.1

    UniProtKB/Swiss-Prot
    O15018
    UniProtKB/TrEMBL
    A0A024RE15
    Conserved Domains (2) summary
    smart00228
    Location:27512833
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:589670
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  7. XM_017009246.1XP_016864735.1  PDZ domain-containing protein 2 isoform X7

    Conserved Domains (2) summary
    smart00228
    Location:24542536
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:258339
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  8. XM_005248271.1XP_005248328.1  PDZ domain-containing protein 2 isoform X5

    See identical proteins and their annotated locations for XP_005248328.1

    Conserved Domains (2) summary
    smart00228
    Location:26112693
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:415496
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  9. XM_017009245.1XP_016864734.1  PDZ domain-containing protein 2 isoform X6

  10. XM_006714460.2XP_006714523.1  PDZ domain-containing protein 2 isoform X7

    Conserved Domains (2) summary
    smart00228
    Location:24542536
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:258339
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  11. XM_005248272.4XP_005248329.1  PDZ domain-containing protein 2 isoform X5

    See identical proteins and their annotated locations for XP_005248329.1

    Conserved Domains (2) summary
    smart00228
    Location:26112693
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:415496
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_015022.2: Suppressed sequence

    Description
    NM_015022.2: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
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