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PDZRN3 PDZ domain containing ring finger 3 [ Homo sapiens (human) ]

Gene ID: 23024, updated on 16-Apr-2024

Summary

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Official Symbol
PDZRN3provided by HGNC
Official Full Name
PDZ domain containing ring finger 3provided by HGNC
Primary source
HGNC:HGNC:17704
See related
Ensembl:ENSG00000121440 MIM:609729; AllianceGenome:HGNC:17704
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
LNX3; SEMCAP3; SEMACAP3
Summary
This gene encodes a member of the LNX (Ligand of Numb Protein-X) family of RING-type ubiquitin E3 ligases. This protein may function in vascular morphogenesis and the differentiation of adipocytes, osteoblasts and myoblasts. This protein may be targeted for degradation by the human papilloma virus E6 protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
Expression
Broad expression in ovary (RPKM 21.4), endometrium (RPKM 16.6) and 20 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
3p13
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (73382431..73624941, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (73423926..73666429, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (73431582..73674092, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986098 Neighboring gene Sharpr-MPRA regulatory region 9383 Neighboring gene GPATCH11 pseudogene 1 Neighboring gene RNA, U6 small nuclear 1270, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:73343679-73344179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20099 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:73533722-73534255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20102 Neighboring gene uncharacterized LOC101927296 Neighboring gene RNA, U7 small nuclear 119 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:73671511-73672025 Neighboring gene PDZRN3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:73697351-73697852 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:73697853-73698352 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71107 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71127 Neighboring gene uncharacterized LOC105377164 Neighboring gene PRDX5 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. 3p interstitial deletion: novel case report and review. Ţuţulan-Cunită AC, et al. J Child Neurol, 2012 Aug. PMID 22290856
  2. Gene expression profiles in primary ovarian serous papillary tumors and normal ovarian epithelium: identification of candidate molecular markers for ovarian cancer diagnosis and therapy. Santin AD, et al. Int J Cancer, 2004 Oct 20. PMID 15305371
  3. Sodium-coupled monocarboxylate transporter 1 interacts with the RING finger- and PDZ domain-containing protein PDZRN3. Otsuka Y, et al. J Physiol Sci, 2019 Jul. PMID 31098988, Free PMC Article
  4. PDZRN3/LNX3 is a novel target of human papillomavirus type 16 (HPV-16) and HPV-18 E6. Thomas M, et al. J Virol, 2015 Jan 15. PMID 25355882, Free PMC Article
  5. Regulation of adipocyte differentiation of 3T3-L1 cells by PDZRN3. Honda T, et al. Am J Physiol Cell Physiol, 2013 Jun 1. PMID 23576576

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Granulysin-mediated reduction of PDZRN3 induces Cx43 gap junctions activity exacerbating skin damage in trichloroethylene hypersensitivity syndrome.
    Title: Granulysin-mediated reduction of PDZRN3 induces Cx43 gap junctions activity exacerbating skin damage in trichloroethylene hypersensitivity syndrome.
  2. PDZRN3 may regulate SMCT1 function by interfering with the interaction between SMCT1 and PDZK1.
    Title: Sodium-coupled monocarboxylate transporter 1 interacts with the RING finger- and PDZ domain-containing protein PDZRN3.
  3. Authors show that HPV-16 and HPV-18 E6 can target PDZRN3 in a PDZ- and proteasome-dependent manner and provide a connection between the papillomavirus life cycle and differentiation-related STAT signaling.
    Title: PDZRN3/LNX3 is a novel target of human papillomavirus type 16 (HPV-16) and HPV-18 E6.
  4. a novel partner of Kidins220/ARMS
    Title: Kidins220/ARMS interacts with Pdzrn3, a protein containing multiple binding domains.
  5. These results indicate that PDZRN3 plays an important role in negative feedback control of BMP-2-induced osteoblast differentiation in C2C12 cells through inhibition of Wnt3a-beta-catenin signaling.
    Title: PDZRN3 negatively regulates BMP-2-induced osteoblast differentiation through inhibition of Wnt signaling.
  6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  7. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: A three-stage genome-wide association study of general cognitive ability: hunting the small effects.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
EBI GWAS Catalog
Impact of ancestry and common genetic variants on QT interval in African Americans.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ11646, FLJ27386

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin-protein transferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in neuromuscular junction development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
involved_in protein ubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in neuromuscular junction IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
E3 ubiquitin-protein ligase PDZRN3
Names
RING-type E3 ubiquitin transferase PDZRN3
ligand of Numb protein X 3
likely ortholog of mouse semaF cytoplasmic domain associated protein 3
semaphorin cytoplasmic domain-associated protein 3
NP_001290068.1
NP_001290069.1
NP_001290070.1
NP_001290071.1
NP_055824.1
XP_016861431.1
XP_054201730.1

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_047128.1 RefSeqGene

    Range
    4981..247491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001303139.2 → NP_001290068.1  E3 ubiquitin-protein ligase PDZRN3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks several exons and uses an alternate 5' terminal exon, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate downstream start codon, compared to variant 1. The resulting protein (isoform 2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AB029018, AK307818, AW661852, DC342349
    UniProtKB/TrEMBL
    B7Z5X9
    Conserved Domains (2) summary
    smart00228
    Location:5 → 36
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:118 → 186
    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. NM_001303140.2 → NP_001290069.1  E3 ubiquitin-protein ligase PDZRN3 isoform 3

    See identical proteins and their annotated locations for NP_001290069.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several exons and uses an alternate 5' terminal exon, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an in-frame downstream start codon, compared to variant 1. The resulting protein (isoform 3) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AB029018, AK294761, AW661852
    Consensus CDS
    CCDS77770.1
    UniProtKB/TrEMBL
    B7Z2I8, E7ENB6
    Related
    ENSP00000418484.1, ENST00000466780.5
    Conserved Domains (1) summary
    cd00992
    Location:77 → 145
    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. NM_001303141.2 → NP_001290070.1  E3 ubiquitin-protein ligase PDZRN3 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks several exons and uses an alternate 5' terminal exon, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate downstream start codon, compared to variant 1. The resulting protein (isoform 4) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AB029018, AK299275, AW661852
    UniProtKB/TrEMBL
    B7Z5Q3, B7ZAC9
    Conserved Domains (2) summary
    smart00228
    Location:29 → 60
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:142 → 210
    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. NM_001303142.2 → NP_001290071.1  E3 ubiquitin-protein ligase PDZRN3 isoform 5

    See identical proteins and their annotated locations for NP_001290071.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks several exons and uses an alternate 5' terminal exon, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate downstream start codon, compared to variant 1. The resulting protein (isoform 5) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AB029018, AK299560, AW661852, DC370885
    Consensus CDS
    CCDS77771.1
    UniProtKB/TrEMBL
    B7Z5X9, B7ZAG0
    Related
    ENSP00000418624.1, ENST00000479530.5
    Conserved Domains (2) summary
    cd00992
    Location:137 → 205
    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) ...
    cl00117
    Location:20 → 53
    PDZ; PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. ...

  5. NM_015009.3 → NP_055824.1  E3 ubiquitin-protein ligase PDZRN3 isoform 1

    See identical proteins and their annotated locations for NP_055824.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB029018, AC117489, AW661852, DB727809
    Consensus CDS
    CCDS33789.1
    UniProtKB/Swiss-Prot
    A7MCZ6, Q8N2N7, Q96CC2, Q9NSQ2, Q9UPQ7
    UniProtKB/TrEMBL
    B2RWP2
    Related
    ENSP00000263666.4, ENST00000263666.9
    Conserved Domains (4) summary
    smart00228
    Location:246 → 338
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00162
    Location:17 → 57
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    cd00992
    Location:420 → 488
    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) ...
    cl19105
    Location:69 → 132
    Sina; Seven in absentia (Sina) protein family, C-terminal substrate binding domain; composed of the Drosophila Sina protein, the mammalian Sina homolog (Siah), the plant protein SINAT5, and similar proteins. Sina, Siah and SINAT5 are RING-containing proteins ...

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    73382431..73624941 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005942.3 → XP_016861431.1  E3 ubiquitin-protein ligase PDZRN3 isoform X1

    UniProtKB/TrEMBL
    B2RWP2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    73423926..73666429 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345755.1 → XP_054201730.1  E3 ubiquitin-protein ligase PDZRN3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UPQ7.2 GenPept UniProtKB/Swiss-Prot:Q9UPQ7

Gene LinkOut

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