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

Gene ID: 23037, updated on 17-Jun-2024

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; AllianceGenome:HGNC:18486
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
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Genomic context

See PDZD2 in Genome Data Viewer
Location:
5p13.3
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (31639131..32110932)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (31752824..32224543)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (31639238..32111038)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22431 Neighboring gene chromosome 5 open reading frame 22 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:31618177-31618357 Neighboring gene RNA, U6 small nuclear 363, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31680333-31680851 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31680852-31681369 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:31716787-31717309 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:31753742-31754275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22434 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:31780232-31780511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31798873-31799374 Neighboring gene small nucleolar RNA U13 Neighboring gene RNA, U6 small nuclear 358, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31853436-31854109 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:31854110-31854782 Neighboring gene uncharacterized LOC124900953 Neighboring gene RNA, U6 small nuclear 760, pseudogene Neighboring gene ribosomal protein L9 pseudogene 17 Neighboring gene OCT4 hESC enhancer GRCh37_chr5:31877194-31877695 Neighboring gene ribosomal protein L21 pseudogene 56 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31878784-31879741 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:31889301-31889803 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:31889804-31890305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31892991-31893492 Neighboring gene ribosomal protein L5 pseudogene 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31923061-31923560 Neighboring gene mitochondrial import receptor subunit TOM7 homolog Neighboring gene NANOG hESC enhancer GRCh37_chr5:31965348-31965849 Neighboring gene TPT1 pseudogene 5 Neighboring gene microRNA 4279 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:32016671-32017172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:32017173-32017672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:32027139-32027640 Neighboring gene NANOG hESC enhancer GRCh37_chr5:32041483-32042015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:32092735-32093236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:32093237-32093736 Neighboring gene uncharacterized LOC105374711 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:32097810-32099009 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:32125750-32126949 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15953 Neighboring gene golgi phosphoprotein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15954 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • KIAA0300

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in cell-cell junction ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
located_in centriolar satellite IDA
Inferred from Direct Assay
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
located_in extracellular region ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 

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)

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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
    4722..476523
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_178140.4NP_835260.2  PDZ domain-containing protein 2

    See identical proteins and their annotated locations for NP_835260.2

    Status: REVIEWED

    Source sequence(s)
    AB002298, AC022447, AC025178, CA503068
    Consensus CDS
    CCDS34137.1
    UniProtKB/Swiss-Prot
    O15018, Q9BXD4
    Related
    ENSP00000402033.1, ENST00000438447.2
    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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    31639131..32110932
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005248269.5XP_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_011513992.3XP_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) ...
  3. XM_011513994.3XP_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) ...
  4. XM_011513996.3XP_011512298.1  PDZ domain-containing protein 2 isoform X3

    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_011513993.3XP_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_006714460.3XP_006714523.1  PDZ domain-containing protein 2 isoform X4

    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) ...
  7. XM_047416965.1XP_047272921.1  PDZ domain-containing protein 2 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    31752824..32224543
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352108.1XP_054208083.1  PDZ domain-containing protein 2 isoform X1

  2. XM_054352110.1XP_054208085.1  PDZ domain-containing protein 2 isoform X2

  3. XM_054352107.1XP_054208082.1  PDZ domain-containing protein 2 isoform X1

  4. XM_054352111.1XP_054208086.1  PDZ domain-containing protein 2 isoform X3

  5. XM_054352109.1XP_054208084.1  PDZ domain-containing protein 2 isoform X1

  6. XM_054352112.1XP_054208087.1  PDZ domain-containing protein 2 isoform X4

  7. XM_054352113.1XP_054208088.1  PDZ domain-containing protein 2 isoform X5

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.