vcp valosin containing protein [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: vcpprovided by ZNC
Official Full Name: valosin containing proteinprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-5408
See related: Ensembl:ENSDARG00000020008 AllianceGenome:ZFIN:ZDB-GENE-030131-5408
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: CDC48; wu:fd16d05; wu:fj63d11
Summary: Predicted to enable ATP hydrolysis activity and polyubiquitin modification-dependent protein binding activity. Acts upstream of or within chordate embryonic development; locomotory behavior; and regulation of cellular catabolic process. Predicted to be located in cytoplasm and site of double-strand break. Predicted to be part of VCP-NPL4-UFD1 AAA ATPase complex. Predicted to be active in cytosol and nucleus. Is expressed in several structures, including brain; digestive system; eye; fin bud; and trunk musculature. Human ortholog(s) of this gene implicated in several diseases, including Charcot-Marie-Tooth disease type 2Y; Paget's disease of bone; amyotrophic lateral sclerosis type 14; inclusion body myopathy with early-onset Paget disease of bone with or without frontotemporal dementia 1; and inclusion body myositis. Orthologous to human VCP (valosin containing protein). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 5

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	5	NC_007116.7 (41510420..41520582)
105	previous assembly	GRCz10 (GCF_000002035.5)	5	NC_007116.6 (40910267..40920429)

Chromosome 5 - NC_007116.7 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: 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?

Novel insights into the in vivo functions of Vcp and its novel interactor Washc4 and their particular and distinct roles during proteostasis in striated muscle cells.
Title: Loss of the novel Vcp (valosin containing protein) interactor Washc4 interferes with autophagy-mediated proteostasis in striated muscle and leads to myopathy in vivo.
When we introduced CDC48 antisense morpholino oligonucleotides into zebrafish embryos, the morphant embryos were lethal and showed defects in neuronal outgrowth and neurodegeneration.
Title: Protective role of cell division cycle 48 (CDC48) protein against neurodegeneration via ubiquitin-proteasome system dysfunction during zebrafish development.
CDC48 may promote cell cycling and cell proliferation via C-terminal tyrosine phosphorylation during cold acclimation in fish cells
Title: Cold-inducible expression of the cell division cycle gene CDC48 and its promotion of cell proliferation during cold acclimation in zebrafish cells.

Submit: New GeneRIF Correction

General gene information

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Markers

fj63d11.x1 (e-PCR)
- UniSTS:199715

fj97a07.x1 (e-PCR)
- UniSTS:200412

AI721787 (e-PCR)
- UniSTS:206052

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables lipid binding	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables polyubiquitin modification-dependent protein binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in ERAD pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in autophagosome maturation	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagosome maturation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within autophagy	IEA Inferred from Electronic Annotation more info
involved_in autophagy	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within cardiac muscle cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell cycle	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chordate embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in double-strand break repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in endosome to lysosome transport via multivesicular body sorting pathway	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within heart contraction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in interstrand cross-link repair	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within locomotory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in macroautophagy	ISS Inferred from Sequence or Structural Similarity more info
involved_in mitotic spindle disassembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within myofibril assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of proteasomal ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein localization to chromatin	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to endoplasmic reticulum stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrograde protein transport, ER to cytosol	IBA Inferred from Biological aspect of Ancestor more info
involved_in translesion synthesis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of VCP-NPL4-UFD1 AAA ATPase complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in site of double-strand break	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: transitional endoplasmic reticulum ATPase

Names: protein CDC48

NP_958889.1

EC 3.6.4.6

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_201481.1 → NP_958889.1 transitional endoplasmic reticulum ATPase

See identical proteins and their annotated locations for NP_958889.1

Status: PROVISIONAL

Source sequence(s)

BC050488

UniProtKB/Swiss-Prot

Q76KA4, Q7ZU99

Related

ENSDARP00000012048.8, ENSDART00000023779.9

Conserved Domains (6) summary

smart01072
Location:131 → 191

CDC48_2; Cell division protein 48 (CDC48) domain 2

TIGR01243
Location:25 → 764

CDC48; AAA family ATPase, CDC48 subfamily

pfam00004
Location:241 → 370

AAA; ATPase family associated with various cellular activities (AAA)

pfam02359
Location:25 → 107

CDC48_N; Cell division protein 48 (CDC48), N-terminal domain

pfam09336
Location:718 → 760

Vps4_C; Vps4 C terminal oligomerization domain

cl21455
Location:452 → 534

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases