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vps4b vacuolar protein sorting 4 homolog B [ Danio rerio (zebrafish) ]

Gene ID: 393880, updated on 4-Jan-2025

Summary

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Official Symbol
vps4bprovided by ZNC
Official Full Name
vacuolar protein sorting 4 homolog Bprovided by ZNC
Primary source
ZFIN:ZDB-GENE-040426-1235
See related
Ensembl:ENSDARG00000069175 AllianceGenome:ZFIN:ZDB-GENE-040426-1235
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
zgc:63682; ch73-81e6.1
Summary
Predicted to enable ATP binding activity and ATP hydrolysis activity. Acts upstream of or within odontogenesis. Predicted to be located in late endosome membrane. Is expressed in ceratobranchial 5 primary tooth; pharyngeal arch 3-7; and pharyngeal pouch. Orthologous to human VPS4B (vacuolar protein sorting 4 homolog B). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs
human mouse all
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Genomic context

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See vps4b in Genome Data Viewer
Location:
chromosome: 2
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 2 NC_007113.7 (13255986..13333934, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 2 NC_007113.6 (13573200..13651169, complement)

Chromosome 2 - NC_007113.7Genomic Context describing neighboring genes Neighboring gene BCL2 apoptosis regulator b Neighboring gene 3-ketodihydrosphingosine reductase Neighboring gene uncharacterized LOC103909876 Neighboring gene neuromedin U receptor 1b

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. A splicing mutation in VPS4B causes dentin dysplasia I. Yang Q, et al. J Med Genet, 2016 Sep. PMID 27247351
  2. Mutagenesis Screen Identifies agtpbp1 and eps15L1 as Essential for T lymphocyte Development in Zebrafish. Seiler C, et al. PLoS One, 2015. PMID 26161877, Free PMC Article
  3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Clone Names

  • MGC63682

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within odontogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in late endosome membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
vacuolar protein sorting-associated protein 4B
Names
vacuolar protein sorting 4 homolog b-like
vacuolar protein sorting 4b homolog B
NP_001094432.1
NP_001278351.1
XP_009296349.1
XP_009296350.1

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)

  1. NM_001100962.1 → NP_001094432.1  vacuolar protein sorting-associated protein 4B

    See identical proteins and their annotated locations for NP_001094432.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    CU207344
    UniProtKB/TrEMBL
    A0A8M1P1A0, A5WWM0
    Related
    ENSDARP00000074209.5, ENSDART00000079757.6
    Conserved Domains (5) summary
    smart00382
    Location:159 → 295
    AAA; ATPases associated with a variety of cellular activities
    cd02678
    Location:5 → 68
    MIT_VPS4; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.
    pfam00004
    Location:163 → 293
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam09336
    Location:374 → 434
    Vps4_C; Vps4 C terminal oligomerization domain
    cl21455
    Location:128 → 182
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  2. NM_001291422.1 → NP_001278351.1  vacuolar protein sorting-associated protein 4B

    See identical proteins and their annotated locations for NP_001278351.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    CU207344
    UniProtKB/TrEMBL
    A0A8M1P1A0, A5WWM0
    Related
    ENSDARP00000111799.2, ENSDART00000127693.4
    Conserved Domains (5) summary
    smart00382
    Location:159 → 295
    AAA; ATPases associated with a variety of cellular activities
    cd02678
    Location:5 → 68
    MIT_VPS4; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.
    pfam00004
    Location:163 → 293
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam09336
    Location:374 → 434
    Vps4_C; Vps4 C terminal oligomerization domain
    cl21455
    Location:128 → 182
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

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

  1. NC_007113.7 Reference GRCz11 Primary Assembly

    Range
    13255986..13333934 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009298075.4 → XP_009296350.1  vacuolar protein sorting-associated protein 4B isoform X2

    UniProtKB/TrEMBL
    A0A0R4IPK7, A0A8M3AWN2
    Related
    ENSDARP00000136647.1, ENSDART00000168258.2
    Conserved Domains (5) summary
    smart00382
    Location:229 → 365
    AAA; ATPases associated with a variety of cellular activities
    pfam00004
    Location:233 → 363
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam09336
    Location:444 → 504
    Vps4_C; Vps4 C terminal oligomerization domain
    cl00299
    Location:75 → 138
    MIT; MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar ...
    cl21455
    Location:198 → 252
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  2. XM_009298074.4 → XP_009296349.1  vacuolar protein sorting-associated protein 4B isoform X1

    UniProtKB/TrEMBL
    A0A8M3AZR5
    Conserved Domains (6) summary
    smart00382
    Location:237 → 373
    AAA; ATPases associated with a variety of cellular activities
    COG0457
    Location:8 → 118
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    pfam00004
    Location:241 → 371
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam09336
    Location:452 → 512
    Vps4_C; Vps4 C terminal oligomerization domain
    cl00299
    Location:86 → 146
    MIT; MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar ...
    cl21455
    Location:206 → 260
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
Nucleotide Protein Strain
Heading Accession and Version

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