Pdzrn3 PDZ domain containing RING finger 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pdzrn3provided by RGD
Official Full Name: PDZ domain containing RING finger 3provided by RGD
Primary source: RGD:1305250
See related: EnsemblRapid:ENSRNOG00000057556 AllianceGenome:RGD:1305250
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in neuromuscular junction development and protein ubiquitination. Predicted to be located in cytoplasm. Predicted to be active in neuromuscular junction. Orthologous to human PDZRN3 (PDZ domain containing ring finger 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Muscle (RPKM 245.3), Adrenal (RPKM 175.6) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q34

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (135327082..135553294, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (133770736..133996959, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (133717139..133951282, complement)

Chromosome 4 - NC_086022.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Data suggest that Pdzrn3 mediates endocytosis of dephosphorylated CLDN16 and represents an important component of CLDN16-trafficking machinery in renal tube epithelial cells. (Pdzrn3 = PDZ domain containing RING finger 3 protein; CLDN16 = claudin 16)
Title: The RING finger- and PDZ domain-containing protein PDZRN3 controls localization of the Mg(2+) regulator claudin-16 in renal tube epithelial cells.
a novel partner of Kidins220/ARMS
Title: Kidins220/ARMS interacts with Pdzrn3, a protein containing multiple binding domains.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH128427 (e-PCR)
- UniSTS:211735

AI008935 (e-PCR)
- UniSTS:250681

D4Rat58 (e-PCR), detects polymorphism
- UniSTS:118852

RH141666 (e-PCR)
- UniSTS:223659

BF395872 (e-PCR)
- UniSTS:245434

RH129369 (e-PCR)
- UniSTS:212676

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-protein transferase activity	ISO Inferred from Sequence Orthology 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 neuromuscular junction development	IEA Inferred from Electronic Annotation more info
involved_in neuromuscular junction development	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology 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
located_in neuromuscular junction	IEA Inferred from Electronic Annotation more info
located_in neuromuscular junction	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase PDZRN3

Names: PDZ domain-containing RING finger protein 3; RING-type E3 ubiquitin transferase PDZRN3; semaphorin cytoplasmic domain-associated protein 3

NP_001258180.1

EC 2.3.2.27

XP_017448131.1

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.

mRNA and Protein(s)

NM_001271251.1 → NP_001258180.1 E3 ubiquitin-protein ligase PDZRN3

Status: VALIDATED

Source sequence(s)

FM040449, JAXUCZ010000004

UniProtKB/Swiss-Prot

P68907

UniProtKB/TrEMBL

A0A0G2K4K7

Related

ENSRNOP00000073080.2, ENSRNOT00000090506.3

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:424 → 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 ...