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

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; 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

Location:: 3p13

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (73382431..73624941, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (73423926..73666429, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (73431582..73674092, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
a novel partner of Kidins220/ARMS
Title: Kidins220/ARMS interacts with Pdzrn3, a protein containing multiple binding domains.
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.
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.
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.

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Phenotypes

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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 EBI GWAS CatalogPubMed
Impact of ancestry and common genetic variants on QT interval in African Americans. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A002G41 (e-PCR)
- UniSTS:16939

RH122545 (e-PCR)
- UniSTS:138547

SHGC-77092 (e-PCR)
- UniSTS:58947

RH120254 (e-PCR)
- UniSTS:132710

SHGC-77111 (e-PCR)
- UniSTS:29841

SHGC-77094 (e-PCR)
- UniSTS:30641

SHGC-58565 (e-PCR)
- UniSTS:94400

SHGC-143591 (e-PCR)
- UniSTS:171970

SHGC-17226 (e-PCR)
- UniSTS:77780

RH103942 (e-PCR)
- UniSTS:98267

RH12030 (e-PCR)
- UniSTS:32510

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

EC 2.3.2.27

NP_001290069.1

EC 2.3.2.27

NP_001290070.1

EC 2.3.2.27

NP_001290071.1

EC 2.3.2.27

NP_055824.1

EC 2.3.2.27

XP_016861431.1

EC 2.3.2.27

XP_054201730.1

EC 2.3.2.27

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

NG_047128.1 RefSeqGene

Range

4981..247491

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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) ...
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) ...
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) ...
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. ...
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 ...