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

    Gene ID: 393880, updated on 9-Dec-2024

    Summary

    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 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, Dec 2024]
    Orthologs
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    Genomic context

    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

    Expression

    • 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

    General gene information

    Clone Names

    • MGC63682

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables ATP binding  
    enables ATP hydrolysis activity  
    enables nucleotide binding  
    Component Evidence Code Pubs
    located_in late endosome membrane  

    General protein information

    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)

    NEW Try the new Transcript table

    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_001100962.1NP_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:159295
      AAA; ATPases associated with a variety of cellular activities
      cd02678
      Location:568
      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:163293
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam09336
      Location:374434
      Vps4_C; Vps4 C terminal oligomerization domain
      cl21455
      Location:128182
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
    2. NM_001291422.1NP_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:159295
      AAA; ATPases associated with a variety of cellular activities
      cd02678
      Location:568
      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:163293
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam09336
      Location:374434
      Vps4_C; Vps4 C terminal oligomerization domain
      cl21455
      Location:128182
      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_009298075.4XP_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:229365
      AAA; ATPases associated with a variety of cellular activities
      pfam00004
      Location:233363
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam09336
      Location:444504
      Vps4_C; Vps4 C terminal oligomerization domain
      cl00299
      Location:75138
      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:198252
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
    2. XM_009298074.4XP_009296349.1  vacuolar protein sorting-associated protein 4B isoform X1

      UniProtKB/TrEMBL
      A0A8M3AZR5
      Conserved Domains (6) summary
      smart00382
      Location:237373
      AAA; ATPases associated with a variety of cellular activities
      COG0457
      Location:8118
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      pfam00004
      Location:241371
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam09336
      Location:452512
      Vps4_C; Vps4 C terminal oligomerization domain
      cl00299
      Location:86146
      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:206260
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
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