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UFD1 ubiquitin recognition factor in ER associated degradation 1 [ Homo sapiens (human) ]

Gene ID: 7353, updated on 12-Oct-2019

Summary

Official Symbol
UFD1provided by HGNC
Official Full Name
ubiquitin recognition factor in ER associated degradation 1provided by HGNC
Primary source
HGNC:HGNC:12520
See related
Ensembl:ENSG00000070010 MIM:601754
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UFD1L
Summary
The protein encoded by this gene forms a complex with two other proteins, nuclear protein localization-4 and valosin-containing protein, and this complex is necessary for the degradation of ubiquitinated proteins. In addition, this complex controls the disassembly of the mitotic spindle and the formation of a closed nuclear envelope after mitosis. Mutations in this gene have been associated with Catch 22 syndrome as well as cardiac and craniofacial defects. Alternative splicing results in multiple transcript variants encoding different isoforms. A related pseudogene has been identified on chromosome 18. [provided by RefSeq, Jun 2009]
Expression
Ubiquitous expression in bone marrow (RPKM 14.2), testis (RPKM 13.8) and 25 other tissues See more
Orthologs

Genomic context

See UFD1 in Genome Data Viewer
Location:
22q11.21
Exon count:
12
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 22 NC_000022.11 (19449911..19479193, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (19437464..19466818, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L40 Neighboring gene chromosome 22 open reading frame 39 Neighboring gene uncharacterized LOC105372860 Neighboring gene cell division cycle 45 Neighboring gene claudin 5

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpu vpu The VCP-UFD1L-NPL4 complex is required for HIV-1 Vpu-induced CD4 degradation in the ER-associated degradation pathway. The ATPase activity of VCP and ubiquitin binding to UFD1L are important for CD4 degradation by Vpu PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • DNA Damage Bypass, organism-specific biosystem (from REACTOME)
    DNA Damage Bypass, organism-specific biosystemIn addition to various processes for removing lesions from the DNA, cells have developed specific mechanisms for tolerating unrepaired damage during the replication of the genome. These mechanisms ar...
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Deubiquitination, organism-specific biosystem (from REACTOME)
    Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
  • HRD1/SEL1 ERAD complex, organism-specific biosystem (from KEGG)
    HRD1/SEL1 ERAD complex, organism-specific biosystemStructural complex; Genetic information processing; Protein processing
  • HRD1/SEL1 ERAD complex, conserved biosystem (from KEGG)
    HRD1/SEL1 ERAD complex, conserved biosystemStructural complex; Genetic information processing; Protein processing
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Protein processing in endoplasmic reticulum, organism-specific biosystem (from KEGG)
    Protein processing in endoplasmic reticulum, organism-specific biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...
  • Protein processing in endoplasmic reticulum, conserved biosystem (from KEGG)
    Protein processing in endoplasmic reticulum, conserved biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...
  • Translesion Synthesis by POLH, organism-specific biosystem (from REACTOME)
    Translesion Synthesis by POLH, organism-specific biosystemDNA polymerase eta (POLH) consists of 713 amino acids and can bypass thymidine-thymidine dimers, correctly adding two dAMPs opposite to the lesion. Mutations in the POLH gene result in the loss of th...
  • Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template, organism-specific biosystem (from REACTOME)
    Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template, organism-specific biosystemUbiquitous environmental and endogenous genotoxic agents cause DNA lesions that can interfere with normal DNA metabolism including DNA replication, eventually resulting in mutations that lead to carc...
  • Ub-specific processing proteases, organism-specific biosystem (from REACTOME)
    Ub-specific processing proteases, organism-specific biosystemUb-specific processing proteases (USPs) are the largest of the DUB families with more than 50 members in humans. The USP catalytic domain varies considerably in size and consists of six conserved mo...
  • p97-Ufd1-Npl4 complex, organism-specific biosystem (from KEGG)
    p97-Ufd1-Npl4 complex, organism-specific biosystemStructural complex; Genetic information processing; Protein processing
  • p97-Ufd1-Npl4 complex, conserved biosystem (from KEGG)
    p97-Ufd1-Npl4 complex, conserved biosystemStructural complex; Genetic information processing; Protein processing

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATPase binding IEA
Inferred from Electronic Annotation
more info
 
K48-linked polyubiquitin modification-dependent protein binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
signaling receptor binding IEA
Inferred from Electronic Annotation
more info
 
thiol-dependent ubiquitin-specific protease activity TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
UFD1-NPL4 complex IPI
Inferred from Physical Interaction
more info
PubMed 
VCP-NPL4-UFD1 AAA ATPase complex IDA
Inferred from Direct Assay
more info
PubMed 
VCP-NPL4-UFD1 AAA ATPase complex ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus HDA PubMed 

General protein information

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)

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_001035247.3NP_001030324.2  ubiquitin recognition factor in ER-associated degradation protein 1 isoform B

    See identical proteins and their annotated locations for NP_001030324.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region that results in a frameshift, compared to variant 1. The encoded isoform (B) has a distinct C-terminus and is shorter than isoform A.
    Source sequence(s)
    AC000068, AK225877, AW131352, CB128364, DB496066, DB570679
    Consensus CDS
    CCDS33600.2
    UniProtKB/Swiss-Prot
    Q92890
    Related
    ENSP00000382439.1, ENST00000399523.5
    Conserved Domains (1) summary
    pfam03152
    Location:19193
    UFD1; Ubiquitin fusion degradation protein UFD1
  2. NM_001362910.2NP_001349839.1  ubiquitin recognition factor in ER-associated degradation protein 1 isoform C

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' region and is predicted to use a downstream start codon compared to variant 1. The encoded isoform (C) has a shorter N-terminus compared to isoform A.
    Source sequence(s)
    AC000068, AC000087
    Conserved Domains (1) summary
    pfam03152
    Location:14188
    UFD1; Ubiquitin fusion degradation protein UFD1
  3. NM_005659.7NP_005650.2  ubiquitin recognition factor in ER-associated degradation protein 1 isoform A

    See identical proteins and their annotated locations for NP_005650.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1)encodes the longest isoform (A).
    Source sequence(s)
    AC000068, AW131352, BC005087, CB128364, DB570679
    Consensus CDS
    CCDS13761.1
    UniProtKB/Swiss-Prot
    Q92890
    UniProtKB/TrEMBL
    Q541A5
    Related
    ENSP00000263202.9, ENST00000263202.15
    Conserved Domains (1) summary
    pfam03152
    Location:19193
    UFD1; Ubiquitin fusion degradation protein UFD1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p13 Primary Assembly

    Range
    19449911..19479193 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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