nme3 NME/NM23 nucleoside diphosphate kinase 3 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: nme3provided by ZNC
Official Full Name: NME/NM23 nucleoside diphosphate kinase 3provided by ZNC
Primary source: ZFIN:ZDB-GENE-000210-34
See related: Ensembl:ENSDARG00000100990 AllianceGenome:ZFIN:ZDB-GENE-000210-34
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: ndpkz3; NDPK-Z3; NM23-Z3; zgc:92672; wu:fa99f09
Summary: Predicted to enable nucleoside diphosphate kinase activity. Acts upstream of or within positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway. Is expressed in several structures, including brain; digestive system; male organism; pleuroperitoneal region; and tail bud. Orthologous to human NME3 (NME/NM23 nucleoside diphosphate kinase 3). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 3

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	3	NC_007114.7 (15990547..16000127, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	3	NC_007114.6 (15840754..15850327, complement)

Chromosome 3 - NC_007114.7 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?

depletion of nme3 in zebrafish and Xenopus resulted in typical ciliopathy-associated phenotypes, such as renal malformations and left-right asymmetry defects.
Title: The nucleoside-diphosphate kinase NME3 associates with nephronophthisis proteins and is required for ciliary function during renal development.

Submit: New GeneRIF Correction

General gene information

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Markers

fa99f09.x1 (e-PCR)
- UniSTS:189765

fa99f09.x1 (e-PCR)
- UniSTS:189766

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables kinase activity	IEA Inferred from Electronic Annotation more info
enables nucleoside diphosphate kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables nucleoside diphosphate kinase activity	IEA Inferred from Electronic Annotation more info
enables nucleoside diphosphate kinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within CTP biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within GTP biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within UTP biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in kidney development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondrial fusion	ISS Inferred from Sequence or Structural Similarity more info
involved_in nucleoside triphosphate biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within phosphorylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in ciliary basal body	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in mitochondrial outer membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: nucleoside diphosphate kinase 3

Names: NM23 nucleoside diphosphate kinase 3; non-metastatic cells 3, protein expressed in; nucleoside diphosphate kinase-Z3

NP_571003.1

EC 2.7.4.6

XP_021324964.1

EC 2.7.4.6

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_001362268.1 → NP_001349197.1 nucleoside diphosphate kinase 3 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

BX936333, CR387933, EH446811

UniProtKB/TrEMBL

A0A8M9PJG3

Conserved Domains (1) summary

cd04413
Location:33 → 162

NDPk_I; Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside ...
NM_130928.2 → NP_571003.1 nucleoside diphosphate kinase 3 isoform 2

See identical proteins and their annotated locations for NP_571003.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

BX936333, CR387933, EH440806

UniProtKB/Swiss-Prot

A0A0R4IE65, A7YYJ8, Q9PTF3

Related

ENSDARP00000132457.1, ENSDART00000160628.2

Conserved Domains (2) summary

cd04413
Location:22 → 151

NDPk_I; Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside ...

pfam00334
Location:22 → 156

NDK; Nucleoside diphosphate kinase

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007114.7 Reference GRCz11 Primary Assembly

Range

15990547..16000127 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021469289.1 → XP_021324964.1 nucleoside diphosphate kinase 3 isoform X1

Related

ENSDARP00000139313.1, ENSDART00000160668.2

Conserved Domains (1) summary

cd04413
Location:33 → 162

NDPk_I; Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside ...