U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Ubr4 ubiquitin protein ligase E3 component n-recognin 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313658, updated on 27-Nov-2024

    Summary

    Official Symbol
    Ubr4provided by RGD
    Official Full Name
    ubiquitin protein ligase E3 component n-recognin 4provided by RGD
    Primary source
    RGD:1563121
    See related
    EnsemblRapid:ENSRNOG00000018183 AllianceGenome:RGD:1563121
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Rbaf600
    Summary
    Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in several processes, including negative regulation of HRI-mediated signaling; proteasome-mediated ubiquitin-dependent protein catabolic process; and protein polyubiquitination. Predicted to act upstream of or within protein catabolic process and protein stabilization. Predicted to be located in endosome. Predicted to be active in centrosome; cytosol; and nucleoplasm. Orthologous to human UBR4 (ubiquitin protein ligase E3 component n-recognin 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 264.4), Adrenal (RPKM 251.7) and 9 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Ubr4 in Genome Data Viewer
    Location:
    5q36
    Exon count:
    110
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (156919029..157027127)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (151635825..151743931)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (157848162..157956137)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene MRT4 homolog, ribosome maturation factor Neighboring gene ER membrane protein complex subunit 1 Neighboring gene transfer RNA valine (anticodon AAC) 3 Neighboring gene intermediate filament family orphan 2 Neighboring gene uncharacterized LOC134479043 Neighboring gene microRNA 6215

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables calmodulin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables calmodulin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables ubiquitin protein ligase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ubiquitin protein ligase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables ubiquitin protein ligase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables ubiquitin-protein transferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in cytoplasm protein quality control ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cytoplasm protein quality control ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cytoplasm protein quality control by the ubiquitin-proteasome system IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cytoplasm protein quality control by the ubiquitin-proteasome system ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cytoplasm protein quality control by the ubiquitin-proteasome system ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in endosome organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endosome organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in endosome organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of HRI-mediated signaling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of HRI-mediated signaling ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of HRI-mediated signaling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of fatty acid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of fatty acid biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of autophagy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of autophagy ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of autophagy ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein K11-linked ubiquitination IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein K11-linked ubiquitination ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein K11-linked ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein K27-linked ubiquitination IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein K27-linked ubiquitination ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein K27-linked ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein K48-linked ubiquitination IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein K48-linked ubiquitination ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein K48-linked ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein branched polyubiquitination IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein branched polyubiquitination ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein branched polyubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein stabilization IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within protein stabilization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to oxidative stress IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to oxidative stress ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in ubiquitin-dependent protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    is_active_in centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_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 cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    E3 ubiquitin-protein ligase UBR4
    Names
    N-recognin-4
    RING-type E3 ubiquitin transferase UBR4
    ZUBR1
    retinoblastoma-associated factor 600
    zinc finger UBR1-type protein 1
    NP_001382037.1
    XP_063143863.1
    XP_063143864.1
    XP_063143865.1
    XP_063143866.1
    XP_063143867.1
    XP_063143868.1
    XP_063143869.1
    XP_063143870.1
    XP_063143871.1
    XP_063143872.1
    XP_063143873.1

    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_001395108.1NP_001382037.1  E3 ubiquitin-protein ligase UBR4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/TrEMBL
      A0A0G2JU89
      Related
      ENSRNOP00000069008.3, ENSRNOT00000082138.3
      Conserved Domains (3) summary
      smart00396
      Location:16611728
      ZnF_UBR1; Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway
      pfam12773
      Location:36593703
      DZR; Double zinc ribbon
      pfam13764
      Location:43665162
      E3_UbLigase_R4; E3 ubiquitin-protein ligase UBR4

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      156919029..157027127
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063287801.1XP_063143871.1  E3 ubiquitin-protein ligase UBR4 isoform X9

    2. XM_063287793.1XP_063143863.1  E3 ubiquitin-protein ligase UBR4 isoform X1

    3. XM_063287796.1XP_063143866.1  E3 ubiquitin-protein ligase UBR4 isoform X4

    4. XM_063287794.1XP_063143864.1  E3 ubiquitin-protein ligase UBR4 isoform X2

    5. XM_063287798.1XP_063143868.1  E3 ubiquitin-protein ligase UBR4 isoform X6

    6. XM_063287799.1XP_063143869.1  E3 ubiquitin-protein ligase UBR4 isoform X7

    7. XM_063287797.1XP_063143867.1  E3 ubiquitin-protein ligase UBR4 isoform X5

    8. XM_063287795.1XP_063143865.1  E3 ubiquitin-protein ligase UBR4 isoform X3

      Related
      ENSRNOP00000032156.5, ENSRNOT00000039663.7
    9. XM_063287800.1XP_063143870.1  E3 ubiquitin-protein ligase UBR4 isoform X8

    10. XM_063287803.1XP_063143873.1  E3 ubiquitin-protein ligase UBR4 isoform X11

    11. XM_063287802.1XP_063143872.1  E3 ubiquitin-protein ligase UBR4 isoform X10

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001039026.1: Suppressed sequence

      Description
      NM_001039026.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.