pdzrn3b PDZ domain containing RING finger 3b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: pdzrn3bprovided by ZNC
Official Full Name: PDZ domain containing RING finger 3bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-071022-4
See related: Ensembl:ENSDARG00000073869 AllianceGenome:ZFIN:ZDB-GENE-071022-4
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: pdzrn3
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 and synapse. Is expressed in several structures, including hindbrain neural plate; nervous system; notochord; optic vesicle; and presumptive neural retina. Orthologous to human PDZRN3 (PDZ domain containing ring finger 3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 6

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	6	NC_007117.7 (44244606..44401982, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	6	NC_007117.6 (44247057..44404446, complement)

Chromosome 6 - NC_007117.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin-protein transferase activity	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
acts_upstream_of_or_within protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase PDZRN3-B

Names: E3 ubiquitin-protein ligase PDZRN3; PDZ domain containing RING finger 3; PDZ domain-containing RING finger protein 3-B

NP_001243321.1

EC 2.3.2.27

XP_005166059.1

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_001256392.1 → NP_001243321.1 E3 ubiquitin-protein ligase PDZRN3-B

See identical proteins and their annotated locations for NP_001243321.1

Status: PROVISIONAL

Source sequence(s)

JN108761

UniProtKB/Swiss-Prot

E7FDW2, K9K836

Related

ENSDARP00000101938.2, ENSDART00000114330.4

Conserved Domains (3) summary

smart00228
Location:245 → 337

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

cd00162
Location:17 → 58

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:421 → 489

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_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007117.7 Reference GRCz11 Primary Assembly

Range

44244606..44401982 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005166002.5 → XP_005166059.1 E3 ubiquitin-protein ligase PDZRN3-B isoform X1

UniProtKB/TrEMBL

A0A8M2BDD2

Conserved Domains (2) summary

smart00228
Location:21 → 56

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

cd00992
Location:140 → 208

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) ...