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Aliases for UFD1 Gene

Aliases for UFD1 Gene

  • Ubiquitin Recognition Factor In ER Associated Degradation 1 2 3
  • UFD1L 3 4 5
  • Ubiquitin Fusion Degradation 1 Like (Yeast) 2 5
  • UB Fusion Protein 1 3 4
  • Ubiquitin Recognition Factor In ER-Associated Degradation Protein 1 3
  • Ubiquitin Fusion Degradation Protein 1 Homolog 3
  • Ubiquitin Fusion Degradation 1-Like 2
  • Ubiquitin Fusion Degradation 1 Like 3

External Ids for UFD1 Gene

Previous HGNC Symbols for UFD1 Gene

  • UFD1L

Summaries for UFD1 Gene

Entrez Gene Summary for UFD1 Gene

  • 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]

GeneCards Summary for UFD1 Gene

UFD1 (Ubiquitin Recognition Factor In ER Associated Degradation 1) is a Protein Coding gene. Diseases associated with UFD1 include Velocardiofacial Syndrome and Digeorge Syndrome. Among its related pathways are Deubiquitination and Protein processing in endoplasmic reticulum.

UniProtKB/Swiss-Prot for UFD1 Gene

  • Essential component of the ubiquitin-dependent proteolytic pathway which degrades ubiquitin fusion proteins. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. It may be involved in the development of some ectoderm-derived structures (By similarity). Acts as a negative regulator of type I interferon production via the complex formed with VCP and NPLOC4, which binds to DDX58/RIG-I and recruits RNF125 to promote ubiquitination and degradation of DDX58/RIG-I (PubMed:26471729).

Gene Wiki entry for UFD1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for UFD1 Gene

Genomics for UFD1 Gene

Regulatory Elements for UFD1 Gene

Enhancers for UFD1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH22G019477 1.4 ENCODE dbSUPER 39.6 +0.0 46 3.8 CREB3L1 YBX1 FEZF1 DMAP1 YY1 ZNF143 SP3 NFYC TBX21 MEF2D UFD1 E2F6P1 LOC105372860 TBX1 CLTCL1 ENSG00000273212
GH22G019418 2 FANTOM5 Ensembl ENCODE dbSUPER 27.1 +58.2 58193 6.2 HDGF HNRNPUL1 PKNOX1 CREB3L1 ARNT FEZF1 YY1 ZNF766 KLF13 ZNF263 UFD1 RPL7AP70 CLTCL1 HIRA MRPL40 RN7SL168P
GH22G019429 1.4 ENCODE dbSUPER 25 +47.5 47523 4.7 MLX CREB3L1 AGO1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 LINC01311 DGCR8 UFD1 RPL7AP70 ENSG00000273300 DGCR11 RTL10 ENSG00000273343 DGCR14 CLTCL1
GH22G019360 1.1 ENCODE dbSUPER 30.9 +117.6 117645 2.9 CTCF HDGF PKNOX1 EBF1 RELA POLR2A EED PRDM10 RELB IKZF2 UFD1 CLTCL1 LOC105372860 CDC45 SLC25A1 RN7SL168P LOC105372859
GH22G019463 0.8 ENCODE 37.6 +15.3 15275 1.8 HNRNPUL1 HDAC6 GTF2E2 JUN TSC22D4 NFXL1 FOSL1 ZNF121 GATA3 POLR2A UFD1 MRPL40 ENSG00000273300 CLTCL1 DGCR8 TSSK2 TSSK1A DGCR2 ENSG00000223461 RPL8P5
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around UFD1 on UCSC Golden Path with GeneCards custom track

Promoters for UFD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000143749 -4 3001 CREB3L1 YBX1 FEZF1 DMAP1 YY1 ZNF143 SP3 NFYC TBX21 MEF2D

Genomic Location for UFD1 Gene

Chromosome:
22
Start:
19,449,910 bp from pter
End:
19,479,296 bp from pter
Size:
29,387 bases
Orientation:
Minus strand

Genomic View for UFD1 Gene

Genes around UFD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
UFD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for UFD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for UFD1 Gene

Proteins for UFD1 Gene

  • Protein details for UFD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92890-UFD1_HUMAN
    Recommended name:
    Ubiquitin fusion degradation protein 1 homolog
    Protein Accession:
    Q92890
    Secondary Accessions:
    • A8MW31
    • Q9Y5N0

    Protein attributes for UFD1 Gene

    Size:
    307 amino acids
    Molecular mass:
    34500 Da
    Quaternary structure:
    • Heterodimer with NPLOC4, this heterodimer binds VCP and inhibits Golgi membrane fusion (PubMed:11574150, PubMed:26471729). Interacts with USP13 (PubMed:21571647).

    Three dimensional structures from OCA and Proteopedia for UFD1 Gene

    Alternative splice isoforms for UFD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for UFD1 Gene

Post-translational modifications for UFD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for UFD1 Gene

Domains & Families for UFD1 Gene

Protein Domains for UFD1 Gene

Suggested Antigen Peptide Sequences for UFD1 Gene

Graphical View of Domain Structure for InterPro Entry

Q92890

UniProtKB/Swiss-Prot:

UFD1_HUMAN :
  • Belongs to the UFD1 family.
Family:
  • Belongs to the UFD1 family.
genes like me logo Genes that share domains with UFD1: view

No data available for Gene Families for UFD1 Gene

Function for UFD1 Gene

Molecular function for UFD1 Gene

UniProtKB/Swiss-Prot Function:
Essential component of the ubiquitin-dependent proteolytic pathway which degrades ubiquitin fusion proteins. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. It may be involved in the development of some ectoderm-derived structures (By similarity). Acts as a negative regulator of type I interferon production via the complex formed with VCP and NPLOC4, which binds to DDX58/RIG-I and recruits RNF125 to promote ubiquitination and degradation of DDX58/RIG-I (PubMed:26471729).

Gene Ontology (GO) - Molecular Function for UFD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004843 thiol-dependent ubiquitin-specific protease activity TAS 9063746
GO:0005102 receptor binding IEA --
GO:0005515 protein binding IPI 11574150
GO:0032403 protein complex binding IEA --
GO:0036435 K48-linked polyubiquitin binding IEA --
genes like me logo Genes that share ontologies with UFD1: view
genes like me logo Genes that share phenotypes with UFD1: view

Human Phenotype Ontology for UFD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for UFD1 Gene

MGI Knock Outs for UFD1:

Animal Model Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for UFD1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for UFD1 Gene

Localization for UFD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for UFD1 Gene

Nucleus. Cytoplasm, cytosol.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for UFD1 gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 5
cytosol 5
mitochondrion 3
peroxisome 1

Gene Ontology (GO) - Cellular Components for UFD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 21630459
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0005783 endoplasmic reticulum IDA --
GO:0005829 cytosol IEA --
genes like me logo Genes that share ontologies with UFD1: view

Pathways & Interactions for UFD1 Gene

genes like me logo Genes that share pathways with UFD1: view

Pathways by source for UFD1 Gene

UniProtKB/Swiss-Prot Q92890-UFD1_HUMAN

  • Pathway: Protein degradation; proteasomal ubiquitin-dependent pathway.

Gene Ontology (GO) - Biological Process for UFD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 10024240
GO:0006511 ubiquitin-dependent protein catabolic process IMP,IEA 26471729
GO:0016579 protein deubiquitination TAS --
GO:0030970 retrograde protein transport, ER to cytosol IMP 25660456
GO:0032480 negative regulation of type I interferon production IMP 26471729
genes like me logo Genes that share ontologies with UFD1: view

No data available for SIGNOR curated interactions for UFD1 Gene

Drugs & Compounds for UFD1 Gene

No Compound Related Data Available

Transcripts for UFD1 Gene

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for UFD1

Alternative Splicing Database (ASD) splice patterns (SP) for UFD1 Gene

No ASD Table

Relevant External Links for UFD1 Gene

GeneLoc Exon Structure for
UFD1
ECgene alternative splicing isoforms for
UFD1

Expression for UFD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of UFD1 Gene:

UFD1

mRNA Expression by UniProt/SwissProt for UFD1 Gene:

Q92890-UFD1_HUMAN
Tissue specificity: Found in adult heart, skeletal muscle and pancreas, and in fetal liver and kidney.

Evidence on tissue expression from TISSUES for UFD1 Gene

  • Nervous system(4.8)
  • Heart(4.4)
  • Skin(4.3)
  • Pancreas(2.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for UFD1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • hypothalamus
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • parathyroid
  • pharynx
  • pituitary gland
  • skull
  • thyroid
  • tongue
  • tooth
  • vocal cord
Thorax:
  • aorta
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • thymus
Abdomen:
  • abdominal wall
  • biliary tract
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
Pelvis:
  • pelvis
  • rectum
  • ureter
  • uterus
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • vertebrae
  • white blood cell

Primer Products

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for UFD1 Gene

Orthologs for UFD1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for UFD1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia UFD1L 35
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia UFD1L 35
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia UFD1L 34 35
  • 92.07 (n)
chimpanzee
(Pan troglodytes)
Mammalia UFD1L 35
  • 92 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ufd1l 34
  • 89.9 (n)
mouse
(Mus musculus)
Mammalia Ufd1l 34 35
  • 89.25 (n)
Ufd1 16
platypus
(Ornithorhynchus anatinus)
Mammalia UFD1L 35
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves UFD1L 34 35
  • 82.19 (n)
lizard
(Anolis carolinensis)
Reptilia UFD1L 35
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ufd1l 34
  • 78.18 (n)
zebrafish
(Danio rerio)
Actinopterygii ufd1l 34 35
  • 77.2 (n)
-- 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2823 34
fruit fly
(Drosophila melanogaster)
Insecta Ufd1-like 34 35
  • 61.55 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001307 34
  • 57.86 (n)
worm
(Caenorhabditis elegans)
Secernentea ufd-1 34 35
  • 52.4 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UFD1 34 35 37
  • 50.12 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C02475g 34
  • 49.36 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR662C 34
  • 47.4 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons UFD1 34
  • 56 (n)
soybean
(Glycine max)
eudicotyledons Gma.5658 34
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.13110 34
rice
(Oryza sativa)
Liliopsida Os02g0181800 34
  • 56.94 (n)
Os.18010 34
barley
(Hordeum vulgare)
Liliopsida Hv.10937 34
wheat
(Triticum aestivum)
Liliopsida Ta.7484 34
corn
(Zea mays)
Liliopsida Zm.7574 34
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes ufd1 34
  • 54.02 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 54 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU06856 34
  • 53.36 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6884 34
Species where no ortholog for UFD1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for UFD1 Gene

ENSEMBL:
Gene Tree for UFD1 (if available)
TreeFam:
Gene Tree for UFD1 (if available)

Paralogs for UFD1 Gene

Pseudogenes.org Pseudogenes for UFD1 Gene

genes like me logo Genes that share paralogs with UFD1: view

No data available for Paralogs for UFD1 Gene

Variants for UFD1 Gene

Sequence variations from dbSNP and Humsavar for UFD1 Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs879255633 Pathogenic 19,481,044(+) AGAAC(A/G)GGTAT nc-transcript-variant, upstream-variant-2KB, reference, missense
rs1000095856 -- 19,469,291(+) GTCAG(C/T)GAGGG intron-variant
rs1000193431 -- 19,462,435(+) CTGAG(A/G)CTGAT intron-variant
rs1000331124 -- 19,457,675(+) GCCTG(A/G)TGGCA intron-variant
rs1000366213 -- 19,476,577(+) CACCC(C/T)CCACC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for UFD1 Gene

Variant ID Type Subtype PubMed ID
esv2751940 CNV gain 17911159
esv3575418 CNV gain 25503493
esv3893434 CNV gain 25118596
nsv3558 CNV insertion 18451855
nsv588216 CNV gain 21841781
nsv834124 CNV loss 17160897
nsv834127 CNV loss 17160897

Variation tolerance for UFD1 Gene

Residual Variation Intolerance Score: 24.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.09; 50.86% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for UFD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
UFD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for UFD1 Gene

Disorders for UFD1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for UFD1 Gene - From: Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
velocardiofacial syndrome
  • 22q11 deletion syndrome
digeorge syndrome
  • digeorge sequence
tetralogy of fallot
  • tetrology of fallot
- elite association - COSMIC cancer census association via MalaCards
Search UFD1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for UFD1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
UFD1
genes like me logo Genes that share disorders with UFD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for UFD1 Gene

Publications for UFD1 Gene

  1. UFD1L, a developmentally expressed ubiquitination gene, is deleted in CATCH 22 syndrome. (PMID: 9063746) Pizzuti A. … Dallapiccola B. (Hum. Mol. Genet. 1997) 2 3 4 22 64
  2. Cloning and characterization of the gene encoding human NPL4, a protein interacting with the ubiquitin fusion-degradation protein (UFD1L). (PMID: 11574150) Botta A. … Novelli G. (Gene 2001) 3 4 22 64
  3. A non-canonical role of the p97 complex in RIG-I antiviral signaling. (PMID: 26471729) Hao Q. … Zhou Z. (EMBO J. 2015) 3 4 64
  4. Ubiquitin-recognition protein Ufd1 couples the endoplasmic reticulum (ER) stress response to cell cycle control. (PMID: 21571647) Chen M. … Ronai Z.A. (Proc. Natl. Acad. Sci. U.S.A. 2011) 3 4 64
  5. A family- and population-based study of the UFD1L gene for schizophrenia. (PMID: 18270977) Xie L. … Wei J. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2008) 3 22 64

Products for UFD1 Gene

  • Addgene plasmids for UFD1

Sources for UFD1 Gene

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