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

Gene ID: 23024, updated on 7-Dec-2018

Summary

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
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

Genomic context

See PDZRN3 in Genome Data Viewer
Location:
3p13
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (73382430..73624997, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (73431582..73674072, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986098 Neighboring gene coiled-coil domain containing 75 pseudogene 1 Neighboring gene RNA, U6 small nuclear 1270, pseudogene Neighboring gene uncharacterized LOC101927296 Neighboring gene RNA, U7 small nuclear 119 pseudogene Neighboring gene PDZRN3 antisense RNA 1 Neighboring gene peroxiredoxin 5 pseudogene Neighboring gene uncharacterized LOC105377164

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ11646, FLJ27386

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-protein transferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
neuromuscular junction development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein ubiquitination IEA
Inferred from Electronic Annotation
more info
 
protein ubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cell junction IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
neuromuscular junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 

General protein information

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

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_047128.1 RefSeqGene

    Range
    5001..247492
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001303139.1NP_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/Swiss-Prot
    Q9UPQ7
    Conserved Domains (2) summary
    smart00228
    Location:536
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:118186
    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_001303140.1NP_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, DC412278
    Consensus CDS
    CCDS77770.1
    UniProtKB/Swiss-Prot
    Q9UPQ7
    UniProtKB/TrEMBL
    B7Z2I8, E7ENB6
    Related
    ENSP00000418484.1, ENST00000466780.5
    Conserved Domains (1) summary
    cd00992
    Location:77145
    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_001303141.1NP_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/Swiss-Prot
    Q9UPQ7
    UniProtKB/TrEMBL
    B7Z5Q3
    Conserved Domains (2) summary
    smart00228
    Location:2960
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:142210
    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_001303142.1NP_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/Swiss-Prot
    Q9UPQ7
    UniProtKB/TrEMBL
    B7Z5X9, B7ZAG0
    Related
    ENSP00000418624.1, ENST00000479530.5
    Conserved Domains (2) summary
    cd00992
    Location:137205
    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:2053
    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_015009.3NP_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
    Q9UPQ7
    Related
    ENSP00000263666.4, ENST00000263666.8
    Conserved Domains (4) summary
    smart00228
    Location:246338
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00162
    Location:1757
    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:420488
    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:69132
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    73382430..73624997 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005942.2XP_016861431.1  E3 ubiquitin-protein ligase PDZRN3 isoform X1

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