Human Gene UFD1L (uc002zpm.2) Description and Page Index
  Description: Homo sapiens ubiquitin fusion degradation 1 like (yeast) (UFD1L), transcript variant 1, mRNA.
RefSeq Summary (NM_005659): 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].
Transcript (Including UTRs)
   Position: hg19 chr22:19,437,464-19,466,738 Size: 29,275 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr22:19,438,193-19,466,608 Size: 28,416 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:19,437,464-19,466,738)mRNA (may differ from genome)Protein (307 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: UFD1_HUMAN
DESCRIPTION: RecName: Full=Ubiquitin fusion degradation protein 1 homolog; Short=UB fusion protein 1;
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.
PATHWAY: Protein degradation; proteasomal ubiquitin-dependent pathway.
SUBUNIT: Heterodimer with NPLOC4, this heterodimer binds VCP and inhibits Golgi membrane fusion. Interacts with USP13.
SUBCELLULAR LOCATION: Nucleus (By similarity). Cytoplasm, cytosol (By similarity).
TISSUE SPECIFICITY: Found in adult heart, skeletal muscle and pancreas, and in fetal liver and kidney.
SIMILARITY: Belongs to the UFD1 family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): UFD1L
CDC HuGE Published Literature: UFD1L
Positive Disease Associations: Body Weights and Measures , schizophrenia
Related Studies:
  1. Body Weights and Measures
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  2. schizophrenia
    De Luca A 2001, , American journal of medical genetics. 2001 Aug;105(6):529-33. [PubMed 11496370]
    The results are supportive of UFD1L involvement in the neurodevelopmental origin of schizophrenia and contribute in delineating etiological and pathogenetic mechanism of the schizophrenia subtype related to 22q11.2 deletion syndrome.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 32.60 RPKM in Testis
Total median expression: 783.96 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -53.40130-0.411 Picture PostScript Text
3' UTR -191.40729-0.263 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004854 - UFD1

Pfam Domains:
PF03152 - Ubiquitin fusion degradation protein UFD1

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2YUJ
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q92890
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004843 thiol-dependent ubiquitin-specific protease activity
GO:0005102 receptor binding
GO:0005515 protein binding
GO:0036435 K48-linked polyubiquitin binding
GO:0044877 macromolecular complex binding
GO:0051117 ATPase binding

Biological Process:
GO:0001501 skeletal system development
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0016579 protein deubiquitination
GO:0030970 retrograde protein transport, ER to cytosol
GO:0032480 negative regulation of type I interferon production
GO:0039536 negative regulation of RIG-I signaling pathway
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0070987 error-free translesion synthesis
GO:0071712 ER-associated misfolded protein catabolic process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0034098 VCP-NPL4-UFD1 AAA ATPase complex
GO:0036501 UFD1-NPL4 complex


-  Descriptions from all associated GenBank mRNAs
  LF210540 - JP 2014500723-A/18043: Polycomb-Associated Non-Coding RNAs.
LF338648 - JP 2014500723-A/146151: Polycomb-Associated Non-Coding RNAs.
LF338647 - JP 2014500723-A/146150: Polycomb-Associated Non-Coding RNAs.
LF338646 - JP 2014500723-A/146149: Polycomb-Associated Non-Coding RNAs.
BX648374 - Homo sapiens mRNA; cDNA DKFZp686G24189 (from clone DKFZp686G24189).
BC005087 - Homo sapiens ubiquitin fusion degradation 1 like (yeast), mRNA (cDNA clone MGC:13073 IMAGE:3830774), complete cds.
BX648483 - Homo sapiens mRNA; cDNA DKFZp686N1355 (from clone DKFZp686N1355).
AK225877 - Homo sapiens mRNA for ubiquitin fusion degradation 1-like, clone: FCC123H12.
BC001049 - Homo sapiens ubiquitin fusion degradation 1 like (yeast), mRNA (cDNA clone MGC:1385 IMAGE:3507963), complete cds.
U64444 - Homo sapiens ubiquitin fusion-degradation 1 like protein (UFD1L) mRNA, complete cds.
AK128120 - Homo sapiens cDNA FLJ46241 fis, clone TESTI4018436, highly similar to Ubiquitin fusion degradation protein 1.
AY101594 - Homo sapiens ubiquitin fusion degradation 1-like mRNA, complete cds.
CR456607 - Homo sapiens UFD1L full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.UFD1L).
AF141201 - Homo sapiens ubiquitin fusion-degradation 1 protein (UFD1) mRNA, complete cds.
AJ239058 - Homo sapiens mRNA for ubiquitin fusion degradation 1 protein (ufd1 gene).
CU013203 - Homo sapiens UFD1L, mRNA (cDNA clone IMAGE:100000556), complete cds, with stop codon, in Gateway system.
KJ892354 - Synthetic construct Homo sapiens clone ccsbBroadEn_01748 UFD1L gene, encodes complete protein.
AB528271 - Synthetic construct DNA, clone: pF1KE0550, Homo sapiens UFD1L gene for ubiquitin fusion degradation 1 like, without stop codon, in Flexi system.
AM392868 - Synthetic construct Homo sapiens clone IMAGE:100002100 for hypothetical protein (UFD1L gene).
CU013491 - Homo sapiens UFD1L, mRNA (cDNA clone IMAGE:100000460), complete cds, without stop codon, in Gateway system.
CU674530 - Synthetic construct Homo sapiens gateway clone IMAGE:100018815 5' read UFD1L mRNA.
LF338645 - JP 2014500723-A/146148: Polycomb-Associated Non-Coding RNAs.
AK310950 - Homo sapiens cDNA, FLJ17992.
AK315998 - Homo sapiens cDNA, FLJ78897 complete cds, highly similar to Ubiquitin fusion degradation protein 1 homolog.
AK304734 - Homo sapiens cDNA FLJ59614 complete cds, highly similar to Ubiquitin fusion degradation protein 1 homolog.
LF338640 - JP 2014500723-A/146143: Polycomb-Associated Non-Coding RNAs.
AK308786 - Homo sapiens cDNA, FLJ98827.
LF338636 - JP 2014500723-A/146139: Polycomb-Associated Non-Coding RNAs.
LF210541 - JP 2014500723-A/18044: Polycomb-Associated Non-Coding RNAs.
LF338635 - JP 2014500723-A/146138: Polycomb-Associated Non-Coding RNAs.
JD409107 - Sequence 390131 from Patent EP1572962.
MA446117 - JP 2018138019-A/18043: Polycomb-Associated Non-Coding RNAs.
MA574225 - JP 2018138019-A/146151: Polycomb-Associated Non-Coding RNAs.
MA574224 - JP 2018138019-A/146150: Polycomb-Associated Non-Coding RNAs.
MA574223 - JP 2018138019-A/146149: Polycomb-Associated Non-Coding RNAs.
MA574222 - JP 2018138019-A/146148: Polycomb-Associated Non-Coding RNAs.
MA574217 - JP 2018138019-A/146143: Polycomb-Associated Non-Coding RNAs.
MA574213 - JP 2018138019-A/146139: Polycomb-Associated Non-Coding RNAs.
MA446118 - JP 2018138019-A/18044: Polycomb-Associated Non-Coding RNAs.
MA574212 - JP 2018138019-A/146138: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q92890 (Reactome details) participates in the following event(s):

R-HSA-5654985 SPRTN recruits VCP to monoUb:K164-PCNA associated with POLH
R-HSA-6781922 USP13 binds UFD1L:SKP2
R-HSA-5654989 SPRTN:VCP-mediated release of POLH from monoUb:K164-PCNA
R-HSA-110320 Translesion Synthesis by POLH
R-HSA-5689880 Ub-specific processing proteases
R-HSA-110313 Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template
R-HSA-5688426 Deubiquitination
R-HSA-73893 DNA Damage Bypass
R-HSA-597592 Post-translational protein modification
R-HSA-73894 DNA Repair
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: NM_005659, NP_005650, Q92890, Q9Y5N0, UFD1_HUMAN
UCSC ID: uc002zpm.2
RefSeq Accession: NM_005659
Protein: Q92890 (aka UFD1_HUMAN)
CCDS: CCDS13761.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005659.6
exon count: 12CDS single in 3' UTR: no RNA size: 1783
ORF size: 924CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2048.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.