Human Gene UBR4 (ENST00000375254.8) from GENCODE V44
  Description: Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA. (from RefSeq NM_020765)
RefSeq Summary (NM_020765): The protein encoded by this gene is an E3 ubiquitin-protein ligase that interacts with the retinoblastoma-associated protein in the nucleus and with calcium-bound calmodulin in the cytoplasm. The encoded protein appears to be a cytoskeletal component in the cytoplasm and part of the chromatin scaffold in the nucleus. In addition, this protein is a target of the human papillomavirus type 16 E7 oncoprotein. [provided by RefSeq, Aug 2010].
Gencode Transcript: ENST00000375254.8
Gencode Gene: ENSG00000127481.15
Transcript (Including UTRs)
   Position: hg38 chr1:19,074,510-19,210,266 Size: 135,757 Total Exon Count: 106 Strand: -
Coding Region
   Position: hg38 chr1:19,074,832-19,210,248 Size: 135,417 Coding Exon Count: 106 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:19,074,510-19,210,266)mRNA (may differ from genome)Protein (5183 aa)
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OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UBR4_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase UBR4; EC=6.3.2.-; AltName: Full=600 kDa retinoblastoma protein-associated factor; AltName: Full=N-recognin-4; AltName: Full=Retinoblastoma-associated factor of 600 kDa; Short=RBAF600; Short=p600; AltName: Full=Zinc finger UBR1-type protein 1;
FUNCTION: E3 ubiquitin-protein ligase which is a component of the N-end rule pathway. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. Together with clathrin, forms meshwork structures involved in membrane morphogenesis and cytoskeletal organization. Regulates integrin-mediated signaling. May play a role in activation of FAK in response to cell-matrix interactions.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Interacts with RB1 and calmodulin. Interacts with protein E7 from papilloma virus HPV-16, HPV-6B and HPV-11.
INTERACTION: Q96EZ8:MCRS1; NbExp=1; IntAct=EBI-1995940, EBI-348259;
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential). Cytoplasm. Cytoplasm, cytoskeleton. Nucleus. Note=Concentrates at the leading edge of membrane structures involved in actin motility.
SIMILARITY: Belongs to the UBR4 family.
SIMILARITY: Contains 1 UBR-type zinc finger.
SEQUENCE CAUTION: Sequence=CAD43719.1; Type=Erroneous initiation; Sequence=CAI19271.1; Type=Erroneous gene model prediction;

-  Primer design for this transcript
 

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.36 RPKM in Testis
Total median expression: 654.54 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 0.00180.000 Picture PostScript Text
3' UTR -84.20322-0.261 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
IPR025704 - E3_Ub_ligase_UBR4
IPR003126 - Znf_N-recognin

Pfam Domains:
PF13764 - E3 ubiquitin-protein ligase UBR4
PF02207 - Putative zinc finger in N-recognin (UBR box)

ModBase Predicted Comparative 3D Structure on Q5T4S7
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-  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
Genome BrowserGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsemblWormBase 
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 
AlignmentAlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0016032 viral process
GO:0016567 protein ubiquitination
GO:0043312 neutrophil degranulation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0035579 specific granule membrane
GO:0070821 tertiary granule membrane
GO:0101003 ficolin-1-rich granule membrane


-  Descriptions from all associated GenBank mRNAs
  AB007931 - Homo sapiens mRNA for KIAA0462 protein, partial cds.
AF348492 - Homo sapiens p600 mRNA, complete cds.
AK000331 - Homo sapiens cDNA FLJ20324 fis, clone HEP09841, highly similar to AB007931 Homo sapiens mRNA for KIAA0462 protein.
AK092390 - Homo sapiens cDNA FLJ35071 fis, clone PLACE6000191.
AX747516 - Sequence 1041 from Patent EP1308459.
BC018694 - Homo sapiens ubiquitin protein ligase E3 component n-recognin 4, mRNA (cDNA clone IMAGE:3506191), partial cds.
BC073905 - Homo sapiens ubiquitin protein ligase E3 component n-recognin 4, mRNA (cDNA clone IMAGE:4451241), partial cds.
BC063573 - Homo sapiens ubiquitin protein ligase E3 component n-recognin 4, mRNA (cDNA clone IMAGE:3875762), partial cds.
AJ505016 - Homo sapiens mRNA for retinoblastoma-associated factor 600-like protein (RBAF600 gene), mutant allele.
AK025149 - Homo sapiens cDNA: FLJ21496 fis, clone COL05623.
AK022924 - Homo sapiens cDNA FLJ12862 fis, clone NT2RP2003567, highly similar to Homo sapiens mRNA for KIAA0462 protein.
AK298314 - Homo sapiens cDNA FLJ53474 complete cds, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA.
AK123857 - Homo sapiens cDNA FLJ41863 fis, clone OCBBF1000315.
AK026543 - Homo sapiens cDNA: FLJ22890 fis, clone KAT04573, highly similar to AF055010 Homo sapiens clone 24561 unknown mRNA.
AF055010 - Homo sapiens clone 24561 unknown mRNA, partial cds.
AK125800 - Homo sapiens cDNA FLJ43812 fis, clone TESTI4001206.
AK022573 - Homo sapiens cDNA FLJ12511 fis, clone NT2RM2001727, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA.
AK023826 - Homo sapiens cDNA FLJ13764 fis, clone PLACE4000106, highly similar to Homo sapiens mRNA for KIAA0462 protein.
BC007962 - Homo sapiens ubiquitin protein ligase E3 component n-recognin 4, mRNA (cDNA clone IMAGE:4301372), partial cds.
AL049972 - Homo sapiens mRNA; cDNA DKFZp564B122 (from clone DKFZp564B122).
BC096758 - Homo sapiens ubiquitin protein ligase E3 component n-recognin 4, mRNA (cDNA clone IMAGE:4849875), partial cds.
AK001233 - Homo sapiens cDNA FLJ10371 fis, clone NT2RM2001903, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA.
JD190461 - Sequence 171485 from Patent EP1572962.
JD394892 - Sequence 375916 from Patent EP1572962.
JD334994 - Sequence 316018 from Patent EP1572962.
JD389851 - Sequence 370875 from Patent EP1572962.
JD281890 - Sequence 262914 from Patent EP1572962.
JD431735 - Sequence 412759 from Patent EP1572962.
AK302623 - Homo sapiens cDNA FLJ53484 complete cds, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA.
JD253624 - Sequence 234648 from Patent EP1572962.
JD324575 - Sequence 305599 from Patent EP1572962.
JD442403 - Sequence 423427 from Patent EP1572962.
JD447801 - Sequence 428825 from Patent EP1572962.
JD022678 - Sequence 3702 from Patent EP1572962.
JD019647 - Sequence 671 from Patent EP1572962.
AK022322 - Homo sapiens cDNA FLJ12260 fis, clone MAMMA1001551.
DL491421 - Novel nucleic acids.
DL490043 - Novel nucleic acids.
AK056218 - Homo sapiens cDNA FLJ31656 fis, clone NT2RI2004290, weakly similar to Drosophila melanogaster mRNA for calossin protein.
AB037728 - Homo sapiens mRNA for KIAA1307 protein, partial cds.
BC015865 - Homo sapiens zinc finger, UBR1 type 1, mRNA (cDNA clone IMAGE:4691776).
BC041137 - Homo sapiens ubiquitin protein ligase E3 component n-recognin 4, mRNA (cDNA clone IMAGE:5226385), with apparent retained intron.

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

Protein Q5T4S7 (Reactome details) participates in the following event(s):

R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-983147 Release of E3 from polyubiquitinated substrate
R-HSA-6798747 Exocytosis of tertiary granule membrane proteins
R-HSA-6799350 Exocytosis of specific granule membrane proteins
R-HSA-6800426 Exocytosis of ficolin-rich granule membrane proteins
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-6798695 Neutrophil degranulation
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-168249 Innate Immune System
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: A8MPT2, A8MQ33, A8MQB1, ENST00000375254.1, ENST00000375254.2, ENST00000375254.3, ENST00000375254.4, ENST00000375254.5, ENST00000375254.6, ENST00000375254.7, KIAA0462, KIAA1307, NM_020765, O60646, O75050, Q4QRK5, Q5T4S7, Q5T4S8, Q5T4S9, Q5TBN8, Q5TBP2, Q6DKH8, Q6P4A4, Q7L8P7, Q8IXJ4, Q8TDN5, Q8WV67, Q9HA46, Q9P2N9, Q9UG82, RBAF600, UBR4_HUMAN, uc001bbi.1, uc001bbi.2, uc001bbi.3, uc001bbi.4, uc001bbi.5, ZUBR1
UCSC ID: ENST00000375254.8
RefSeq Accession: NM_020765
Protein: Q5T4S7 (aka UBR4_HUMAN)
CCDS: CCDS189.1

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