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Aliases for UFD1 Gene

Aliases for UFD1 Gene

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

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 Meier-Gorlin Syndrome 7. Among its related pathways are Protein processing in endoplasmic reticulum and Regulation of degradation of deltaF508 CFTR in CF.

UniProtKB/Swiss-Prot for UFD1 Gene

  • Essential component of the ubiquitin-dependent proteolytic pathway which degrades ubiquitin fusion proteins. The ternary complex containing UFD1, 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-UFD1-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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for UFD1 Gene

Promoters and enhancers for UFD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22J019477 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 707.1 +0.0 46 3.8 HDGF HNRNPUL1 PKNOX1 CLOCK SMAD1 FOXA2 ARNT ARID4B SIN3A YBX1 UFD1 CDC45 DGCR8 TRMT2A RPL7AP70 DGCR11 ENSG00000273300 RPL8P5 LINC01311 RANBP1
GH22J020078 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 49.2 -602.2 -602225 5.2 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 DGCR8 TRMT2A MED15 LZTR1 RPL7AP70 UFD1 RPL8P5 ENSG00000273300 LOC100420177 ENSG00000243762
GH22J019429 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 45.8 +47.5 47522 4.7 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 ZNF263 MRPL40 HIRA TRMT2A DGCR8 UFD1 LINC01311 RPL7AP70 ENSG00000273300 RPL8P5 ESS2
GH22J019446 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 38 +31.6 31584 2.6 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B HIRA LOC105372860 C22orf39 DGCR8 UFD1 TRMT2A LINC01311 RPL8P5 RPL7AP70 E2F6P1
GH22J019418 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 46.5 +58.2 58192 6.2 HDGF HNRNPUL1 PKNOX1 SMAD1 ARNT IRF4 YY1 POLR2B ZNF766 E2F8 UFD1 TRMT2A DGCR8 RPL7AP70 DGCR11 RPL8P5 ENSG00000273300 LINC01311 RANBP1 ESS2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around UFD1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for UFD1 Gene

Genomic Locations for UFD1 Gene
chr22:19,449,910-19,479,296
(GRCh38/hg38)
Size:
29,387 bases
Orientation:
Minus strand
chr22:19,437,433-19,466,738
(GRCh37/hg19)
Size:
29,306 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 recognition factor in ER-associated degradation protein 1
    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). Interacts with ZFAND2B; probably through VCP (PubMed:24160817).

    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

Gene Families for UFD1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transporters

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

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 UFD1, 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-UFD1-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).

Phenotypes From GWAS Catalog for UFD1 Gene

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 signaling receptor binding IEA --
GO:0005515 protein binding IPI 11574150
GO:0036435 K48-linked polyubiquitin modification-dependent protein binding IEA --
GO:0051117 ATPase 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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for UFD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,HDA 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 IEA,IMP 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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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
Regions:
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

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 34
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia UFD1L 34
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia UFD1L 34 33
  • 92.07 (n)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia UFD1L 34
  • 92 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ufd1l 33
  • 89.9 (n)
mouse
(Mus musculus)
Mammalia Ufd1l 34 33
  • 89.25 (n)
OneToOne
Ufd1 16
platypus
(Ornithorhynchus anatinus)
Mammalia UFD1L 34
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves UFD1L 34 33
  • 82.19 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia UFD1L 34
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ufd1l 33
  • 78.18 (n)
zebrafish
(Danio rerio)
Actinopterygii ufd1l 34 33
  • 77.2 (n)
OneToOne
-- 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2823 33
fruit fly
(Drosophila melanogaster)
Insecta Ufd1-like 34 33
  • 61.55 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001307 33
  • 57.86 (n)
worm
(Caenorhabditis elegans)
Secernentea ufd-1 34 33
  • 52.4 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UFD1 36 34 33
  • 50.12 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C02475g 33
  • 49.36 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR662C 33
  • 47.4 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons UFD1 33
  • 56 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.13110 33
soybean
(Glycine max)
eudicotyledons Gma.5658 33
rice
(Oryza sativa)
Liliopsida Os02g0181800 33
  • 56.94 (n)
Os.18010 33
wheat
(Triticum aestivum)
Liliopsida Ta.7484 33
barley
(Hordeum vulgare)
Liliopsida Hv.10937 33
corn
(Zea mays)
Liliopsida Zm.7574 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes ufd1 33
  • 54.02 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 54 (a)
OneToOne
Cin.6884 33
bread mold
(Neurospora crassa)
Ascomycetes NCU06856 33
  • 53.36 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6884 33
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)
Aminode:
Evolutionary constrained regions (ECRs) for UFD1: view image

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 Variation AA Info Type
rs879255633 pathogenic, Meier-gorlin syndrome 7 19,481,044(-) A/G upstream_transcript_variant
rs1000095856 -- 19,469,291(-) C/T intron_variant
rs1000193431 -- 19,462,435(-) G/A intron_variant
rs1000331124 -- 19,457,675(-) G/A intron_variant
rs1000366213 -- 19,476,577(-) C/T 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)

Additional Variant Information for UFD1 Gene

Human Gene Mutation Database (HGMD)
UFD1
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

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

- elite association - COSMIC cancer census association via MalaCards
Search UFD1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for 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 (Human molecular genetics 1997) 2 3 4 22 58
  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 58
  3. A non-canonical role of the p97 complex in RIG-I antiviral signaling. (PMID: 26471729) Hao Q … Zhou Z (The EMBO journal 2015) 3 4 58
  4. Ubiquitin-recognition protein Ufd1 couples the endoplasmic reticulum (ER) stress response to cell cycle control. (PMID: 21571647) Chen M … Ronai ZA (Proceedings of the National Academy of Sciences of the United States of America 2011) 3 4 58
  5. A family- and population-based study of the UFD1L gene for schizophrenia. (PMID: 18270977) Xie L … Wei J (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2008) 3 22 58

Products for UFD1 Gene

Sources for UFD1 Gene

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