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    Ufd1 ubiquitin recognition factor in ER associated degradation 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 84478, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Ufd1provided by RGD
    Official Full Name
    ubiquitin recognition factor in ER associated degradation 1provided by RGD
    Primary source
    RGD:619822
    See related
    EnsemblRapid:ENSRNOG00000047394 AllianceGenome:RGD:619822
    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
    Summary
    Enables ATPase binding activity and signaling receptor binding activity. Involved in retrograde protein transport, ER to cytosol. Part of UFD1-NPL4 complex and VCP-NPL4-UFD1 AAA ATPase complex. Human ortholog(s) of this gene implicated in DiGeorge syndrome and schizophrenia. Orthologous to human UFD1 (ubiquitin recognition factor in ER associated degradation 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Heart (RPKM 283.3), Adrenal (RPKM 213.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ufd1 in Genome Data Viewer
    Location:
    11q23
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (95665971..95689423, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (82161618..82185107, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (86304836..86328478, complement)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L40 Neighboring gene similar to human chromosome 22 open reading frame 39 Neighboring gene cell division cycle 45 Neighboring gene claudin 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

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    Related articles in PubMed

    1. Absence of mutations in human ubiquitin fusion-degradation protein gene in tetralogy of Fallot. Chung MY, et al. J Mol Med (Berl), 2001 Jun. PMID 11485030
    2. Association study of a promoter polymorphism of UFD1L gene with schizophrenia. De Luca A, et al. Am J Med Genet, 2001 Aug 8. PMID 11496370
    3. A molecular pathway revealing a genetic basis for human cardiac and craniofacial defects. Yamagishi H, et al. Science, 1999 Feb 19. PMID 10024240
    4. Cloning and characterization of the gene encoding human NPL4, a protein interacting with the ubiquitin fusion-degradation protein (UFD1L). Botta A, et al. Gene, 2001 Sep 5. PMID 11574150
    5. Distinct conformations of the protein complex p97-Ufd1-Npl4 revealed by electron cryomicroscopy. Bebeacua C, et al. Proc Natl Acad Sci U S A, 2012 Jan 24. PMID 22232657, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. the p97-Ufd1-Npl4 complex couples ubiquitinated IP(3) receptors to proteasomal degradation and, thus, plays a key role in IP(3) receptor processing
      Title: Involvement of the p97-Ufd1-Npl4 complex in the regulated endoplasmic reticulum-associated degradation of inositol 1,4,5-trisphosphate receptors.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATPase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables K48-linked polyubiquitin modification-dependent protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables K48-linked polyubiquitin modification-dependent protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables polyubiquitin modification-dependent protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signaling receptor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ERAD pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ERAD pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to misfolded protein IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to misfolded protein ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of RIG-I signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of RIG-I signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of RIG-I signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of type I interferon production IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of type I interferon production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of type I interferon production ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in proteasomal protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde protein transport, ER to cytosol EXP
    Inferred from Experiment
    more info
    		 PubMed 
    involved_in retrograde protein transport, ER to cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde protein transport, ER to cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    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
    		  
    Component Evidence Code Pubs
    part_of UFD1-NPL4 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of UFD1-NPL4 complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of UFD1-NPL4 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of VCP-NPL4-UFD1 AAA ATPase complex EXP
    Inferred from Experiment
    more info
    		 PubMed 
    part_of VCP-NPL4-UFD1 AAA ATPase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of VCP-NPL4-UFD1 AAA ATPase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of VCP-NPL4-UFD1 AAA ATPase complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of VCP-NPL4-UFD1 AAA ATPase complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of VCP-NPL4-UFD1 AAA ATPase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin recognition factor in ER-associated degradation protein 1
    Names
    UB fusion protein 1
    ubiquitin fusion degradation 1 like
    ubiquitin fusion degradation protein 1 homolog

    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_053418.2 → NP_445870.1  ubiquitin recognition factor in ER-associated degradation protein 1

      See identical proteins and their annotated locations for NP_445870.1

      Status: VALIDATED

      Source sequence(s)
      AF234601, BC061998, CK599711
      UniProtKB/Swiss-Prot
      Q9ES53
      UniProtKB/TrEMBL
      A0A8I6A8U7
      Related
      ENSRNOP00000067081.3, ENSRNOT00000071493.4
      Conserved Domains (1) summary
      pfam03152
      Location:19 → 193
      UFD1; Ubiquitin fusion degradation protein UFD1

    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_086029.1 Reference GRCr8

      Range
      95665971..95689423 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008768904.4 → XP_008767126.1  ubiquitin recognition factor in ER-associated degradation protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A8U7
      Conserved Domains (1) summary
      pfam03152
      Location:3 → 150
      UFD1; Ubiquitin fusion degradation protein UFD1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001034834.1: Suppressed sequence

      Description
      NM_001034834.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9ES53.1 GenPept UniProtKB/Swiss-Prot:Q9ES53

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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