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    Ufd1 ubiquitin recognition factor in ER-associated degradation 1 [ Mus musculus (house mouse) ]

    Gene ID: 22230, updated on 13-Jan-2025

    Summary

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    Official Symbol
    Ufd1provided by MGI
    Official Full Name
    ubiquitin recognition factor in ER-associated degradation 1provided by MGI
    Primary source
    MGI:MGI:109353
    See related
    Ensembl:ENSMUSG00000005262 AllianceGenome:MGI:109353
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Ufd1l
    Summary
    Enables K48-linked polyubiquitin modification-dependent protein binding activity. Involved in retrograde protein transport, ER to cytosol. Located in cytoplasm. Part of UFD1-NPL4 complex and VCP-NPL4-UFD1 AAA ATPase complex. Is expressed in several structures, including brain; branchial arch; cardiovascular system; forelimb bud; and sensory organ. 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, Jan 2025]
    Expression
    Ubiquitous expression in testis adult (RPKM 28.2), CNS E14 (RPKM 15.4) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ufd1 in Genome Data Viewer
    Location:
    16 A3; 16 11.65 cM
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (18630486..18654011)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (18811736..18835261)

    Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene claudin 5 Neighboring gene cell division cycle 45 Neighboring gene predicted gene, 52240 Neighboring gene STARR-positive B cell enhancer ABC_E763 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:18812268-18812501 Neighboring gene RIKEN cDNA 2510002D24 gene Neighboring gene STARR-positive B cell enhancer ABC_E10892 Neighboring gene mitochondrial ribosomal protein L40 Neighboring gene histone cell cycle regulator

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. UFD1L, a developmentally expressed ubiquitination gene, is deleted in CATCH 22 syndrome. Pizzuti A, et al. Hum Mol Genet, 1997 Feb. PMID 9063746
    2. A common cis-acting sequence in the DiGeorge critical region regulates bi-directional transcription of UFD1L and CDC45L. Kunte A, et al. Mech Dev, 2001 Oct. PMID 11578863
    3. Requirement of CDC45 for postimplantation mouse development. Yoshida K, et al. Mol Cell Biol, 2001 Jul. PMID 11416137, Free PMC Article
    4. The p97/VCP ATPase is critical in muscle atrophy and the accelerated degradation of muscle proteins. Piccirillo R, et al. EMBO J, 2012 Aug 1. PMID 22773186, Free PMC Article
    5. Congenital heart disease in mice deficient for the DiGeorge syndrome region. Lindsay EA, et al. Nature, 1999 Sep 23. PMID 10517636

    See all (58) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The study revealed a regulatory role of the p97-Npl4-Ufd1 complex in regulating a partial degradation of the NF-kappaB subunit p100.
      Title: The Transitional Endoplasmic Reticulum ATPase p97 Regulates the Alternative Nuclear Factor NF-κB Signaling via Partial Degradation of the NF-κB Subunit p100.
    2. structural analysis of the p97-Npl4-Ufd1 interface
      Title: Detailed structural insights into the p97-Npl4-Ufd1 interface.
    3. 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

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (4) 
    • Gene trapped (1) 
    • Targeted (1)  1 citation

    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 MGI

    Function Evidence Code Pubs
    enables ATPase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables K48-linked polyubiquitin modification-dependent protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables signaling receptor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in ERAD pathway EXP
    Inferred from Experiment
    more info
    		 PubMed 
    involved_in ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 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 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 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 ISO
    Inferred from Sequence Orthology
    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 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of VCP-NPL4-UFD1 AAA ATPase complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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_011672.4 → NP_035802.3  ubiquitin recognition factor in ER-associated degradation protein 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and is the protein-coding transcript.
      Source sequence(s)
      AK147138, AW544149, CJ085208
      Consensus CDS
      CCDS28028.1
      UniProtKB/Swiss-Prot
      P70362, Q923C4
      UniProtKB/TrEMBL
      Q9CWQ7
      Related
      ENSMUSP00000005394.7, ENSMUST00000005394.13
      Conserved Domains (1) summary
      pfam03152
      Location:19 → 193
      UFD1; Ubiquitin fusion degradation protein UFD1

    RNA

    1. NR_028403.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction compared to variant 1, that causes a frameshift. This transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is therefore not thought to encode a protein.
      Source sequence(s)
      AK147138, AW544149, CJ053815, CJ085208

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000082.7 Reference GRCm39 C57BL/6J

      Range
      18630486..18654011
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006522006.4 → XP_006522069.1  ubiquitin recognition factor in ER-associated degradation protein 1 isoform X2

      UniProtKB/TrEMBL
      Q9CWQ7
      Conserved Domains (1) summary
      pfam03152
      Location:14 → 188
      UFD1; Ubiquitin fusion degradation protein UFD1

    2. XM_006522007.4 → XP_006522070.1  ubiquitin recognition factor in ER-associated degradation protein 1 isoform X3

      UniProtKB/TrEMBL
      Q9CZJ3
      Conserved Domains (1) summary
      pfam03152
      Location:3 → 150
      UFD1; Ubiquitin fusion degradation protein UFD1

    3. XM_006522005.4 → XP_006522068.1  ubiquitin recognition factor in ER-associated degradation protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P70362, Q923C4
      UniProtKB/TrEMBL
      Q9CWQ7
      Related
      ENSMUSP00000111241.4, ENSMUST00000115578.10
      Conserved Domains (1) summary
      pfam03152
      Location:19 → 193
      UFD1; Ubiquitin fusion degradation protein UFD1
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P70362.2 GenPept UniProtKB/Swiss-Prot:P70362

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