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    ube4b ubiquitination factor E4B, UFD2 homolog (S. cerevisiae) [ Danio rerio (zebrafish) ]

    Gene ID: 170784, updated on 4-Jan-2025

    Summary

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    Official Symbol
    ube4bprovided by ZNC
    Official Full Name
    ubiquitination factor E4B, UFD2 homolog (S. cerevisiae)provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-020205-1
    See related
    Ensembl:ENSDARG00000037017 AllianceGenome:ZFIN:ZDB-GENE-020205-1
    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
    UFD2; zgc:109766
    Summary
    Predicted to enable ubiquitin-ubiquitin ligase activity. Predicted to act upstream of or within ERAD pathway; protein ubiquitination; and ubiquitin-dependent protein catabolic process. Predicted to be located in cytoplasm. Predicted to be part of ubiquitin ligase complex. Is expressed in female organism; heart; and skeletal muscle. Orthologous to human UBE4B (ubiquitination factor E4B). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    human mouse all
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    Genomic context

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    See ube4b in Genome Data Viewer
    Location:
    chromosome: 23
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (29507315..29553712, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 23 NC_007134.6 (29580774..29627171, complement)

    Chromosome 23 - NC_007134.7Genomic Context describing neighboring genes Neighboring gene phosphogluconate dehydrogenase Neighboring gene kinesin family member 1B Neighboring gene nmnat1-rbp7a readthrough Neighboring gene retinol binding protein 7a, cellular Neighboring gene nicotinamide nucleotide adenylyltransferase 1

    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 novel conserved isoform of the ubiquitin ligase UFD2a/UBE4B is expressed exclusively in mature striated muscle cells. Mammen AL, et al. PLoS One, 2011. PMID 22174917, Free PMC Article
    2. The human homologue of the yeast polyubiquitination factor Ufd2p is cleaved by caspase 6 and granzyme B during apoptosis. Mahoney JA, et al. Biochem J, 2002 Feb 1. PMID 11802788, Free PMC Article
    3. Discovery of a genetic module essential for assigning left-right asymmetry in humans and ancestral vertebrates. Szenker-Ravi E, et al. Nat Genet, 2022 Jan. PMID 34903892
    4. Brain transcriptome analysis of a familial Alzheimer's disease-like mutation in the zebrafish presenilin 1 gene implies effects on energy production. Newman M, et al. Mol Brain, 2019 May 3. PMID 31053140, Free PMC Article
    5. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The regulated expression of these UFD2a isoforms most likely imparts divergent functions that are important for myogenesis.
      Title: A novel conserved isoform of the ubiquitin ligase UFD2a/UBE4B is expressed exclusively in mature striated muscle cells.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC109766

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables ubiquitin-protein transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin-ubiquitin ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within ERAD pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of ubiquitin ligase complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin conjugation factor E4 B
    Names
    UBE4B-II splice
    NP_919343.2
    XP_021325394.1
    XP_068072761.1

    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_194362.2 → NP_919343.2  ubiquitin conjugation factor E4 B

      Status: VALIDATED

      Source sequence(s)
      BX571850, EH441473, EH459986, EH552968
      UniProtKB/TrEMBL
      A0A8M1P8S1, F1Q5A9
      Related
      ENSDARP00000053803.6, ENSDART00000053804.8
      Conserved Domains (2) summary
      pfam04564
      Location:1109 → 1179
      U-box; U-box domain
      pfam10408
      Location:472 → 1092
      Ufd2P_core; Ubiquitin elongating factor core

    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_007134.7 Reference GRCz11 Primary Assembly

      Range
      29507315..29553712 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068216660.1 → XP_068072761.1  ubiquitin conjugation factor E4 B isoform X2

      Related
      ENSDARP00000140193.2, ENSDART00000157773.2

    2. XM_021469719.2 → XP_021325394.1  ubiquitin conjugation factor E4 B isoform X1

      UniProtKB/TrEMBL
      A0A8M9PKI9
      Related
      ENSDARP00000105688.3, ENSDART00000126384.3
      Conserved Domains (3) summary
      pfam10408
      Location:638 → 1258
      Ufd2P_core; Ubiquitin elongating factor core
      cd16658
      Location:1271 → 1345
      RING-Ubox_UBE4B; U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 B (UBE4B) and similar proteins
      cl26464
      Location:239 → 413
      Atrophin-1; Atrophin-1 family
    Nucleotide Protein Strain
    Heading Accession and Version

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