Human Gene UHRF2 (ENST00000276893.10_4) from GENCODE V47lift37
  Description: ubiquitin like with PHD and ring finger domains 2, transcript variant 1 (from RefSeq NM_152896.3)
Gencode Transcript: ENST00000276893.10_4
Gencode Gene: ENSG00000147854.18_11
Transcript (Including UTRs)
   Position: hg19 chr9:6,413,199-6,507,054 Size: 93,856 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr9:6,413,491-6,506,179 Size: 92,689 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:6,413,199-6,507,054)mRNA (may differ from genome)Protein (802 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UHRF2_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase UHRF2; EC=6.3.2.-; AltName: Full=Np95/ICBP90-like RING finger protein; Short=Np95-like RING finger protein; AltName: Full=Nuclear protein 97; AltName: Full=Nuclear zinc finger protein Np97; AltName: Full=RING finger protein 107; AltName: Full=Ubiquitin-like PHD and RING finger domain-containing protein 2; AltName: Full=Ubiquitin-like-containing PHD and RING finger domains protein 2;
FUNCTION: E3 ubiquitin-protein ligase that is an intermolecular hub protein in the cell cycle network. Through cooperative DNA and histone binding, may contribute to a tighter epigenetic control of gene expression in differentiated cells. Ubiquitinates cyclins, CCND1 and CCNE1, in an apparently phosphorylation-independent manner and induces G1 arrest. Also ubiquitinates PCNP leading to its degradation by the proteasome. Appears to contribute to tumorigenesis.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Homodimer; disulfide-linked. Binds methylated CpG containing oligonucleotides. Interacts with H3: the interaction has a preference for the 'Lys-9' trimethylated form of H3 (H3K9me3) (By similarity). Interacts with PCNP, HDAC1 and CDK2 (inactive form). Component of a complex at least composed of UHRF2, CDK2 and CCNE1. Interacts directly with CCNE1; the interaction ubiquitinates CCNE1 and appears independent of CCNE1 phosphorylation. Interacts with CCND1; the interaction ubiquitinates CCND1 and appears independent of CCND1 phosphorylation. Interacts with p53/TP53 and RB1.
INTERACTION: P20248:CCNA2; NbExp=2; IntAct=EBI-625304, EBI-457097; P14635:CCNB1; NbExp=2; IntAct=EBI-625304, EBI-495332; P24385:CCND1; NbExp=4; IntAct=EBI-625304, EBI-375001; P24864:CCNE1; NbExp=4; IntAct=EBI-625304, EBI-519526; P24941:CDK2; NbExp=5; IntAct=EBI-625304, EBI-375096; P06400:RB1; NbExp=4; IntAct=EBI-625304, EBI-491274; P04637:TP53; NbExp=3; IntAct=EBI-625304, EBI-366083;
SUBCELLULAR LOCATION: Nucleus. Note=Enriched at pericentric heterochromatin (PH). This localization is dependent on the interaction with H3K9me3 (By similarity).
INDUCTION: Up-regulated in proliferating fetal lung fibroblasts and in U-937 myeloid leukemia cells. Down-regulated in these cells by growth arrest and differentiation. In other cell types which cannot leave the cell cycle, such as tumoral HT-1080 and Hep-G2, levels are consistently up-regulated.
PTM: May be autoubiquitinated; which may lead to proteasomal degradation.
PTM: Phosphorylated. Phosphorylation may be mediated by CDK2.
DISEASE: Note=Associated with various cancers. DNA copy number loss is found in multiple kinds of malignancies originating from the brain, breast, stomach, kidney, hematopoietic tissue and lung.
SIMILARITY: Contains 1 PHD-type zinc finger.
SIMILARITY: Contains 2 RING-type zinc fingers.
SIMILARITY: Contains 1 ubiquitin-like domain.
SIMILARITY: Contains 1 YDG domain.
SEQUENCE CAUTION: Sequence=CAH74120.1; Type=Erroneous gene model prediction; Sequence=CAI13295.1; Type=Erroneous gene model prediction;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 11.97 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 330.68 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 -170.10292-0.583 Picture PostScript Text
3' UTR -204.50875-0.234 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
IPR021991 - DUF3590
IPR003105 - SRA_YDG
IPR000626 - Ubiquitin
IPR019955 - Ubiquitin_supergroup
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00240 - Ubiquitin family
PF00628 - PHD-finger
PF02182 - SAD/SRA domain
PF12148 - Tandem tudor domain within UHRF1

SCOP Domains:
88697 - PUA domain-like
54236 - Ubiquitin-like
57850 - RING/U-box
57903 - FYVE/PHD zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WY8 - NMR MuPIT 1Z6U - X-ray MuPIT 2E6S - NMR MuPIT 3OLN - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q96PU4
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0042393 histone binding
GO:0046872 metal ion binding
GO:0061630 ubiquitin protein ligase activity

Biological Process:
GO:0007049 cell cycle
GO:0008283 cell proliferation
GO:0010216 maintenance of DNA methylation
GO:0016567 protein ubiquitination
GO:0030154 cell differentiation
GO:0051726 regulation of cell cycle
GO:0051865 protein autoubiquitination
GO:0071158 positive regulation of cell cycle arrest
GO:0090308 regulation of methylation-dependent chromatin silencing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005720 nuclear heterochromatin


-  Descriptions from all associated GenBank mRNAs
  BC028397 - Homo sapiens ubiquitin-like with PHD and ring finger domains 2, mRNA (cDNA clone MGC:33463 IMAGE:4797830), complete cds.
AK308433 - Homo sapiens cDNA, FLJ98381.
AF274049 - Homo sapiens nuclear zinc finger protein Np97 (UHRF2) mRNA, complete cds.
AB071698 - Homo sapiens NIRF mRNA for Np95-like ring finger protein, complete cds.
EU176602 - Synthetic construct Homo sapiens clone IMAGE:100011425; FLH179002.01L; RZPDo839D04254D ubiquitin-like, containing PHD and RING finger domains, 2 (UHRF2) gene, encodes complete protein.
EU176286 - Synthetic construct Homo sapiens clone IMAGE:100006403; FLH179006.01X; RZPDo839E01251D ubiquitin-like, containing PHD and RING finger domains, 2 (UHRF2) gene, encodes complete protein.
AB385208 - Synthetic construct DNA, clone: pF1KB9392, Homo sapiens UHRF2 gene for E3 ubiquitin-protein ligase UHRF2, complete cds, without stop codon, in Flexi system.
JD228735 - Sequence 209759 from Patent EP1572962.
JD422402 - Sequence 403426 from Patent EP1572962.
JD478345 - Sequence 459369 from Patent EP1572962.
JD396345 - Sequence 377369 from Patent EP1572962.
AK122730 - Homo sapiens cDNA FLJ16243 fis, clone HCHON2000323, highly similar to Ubiquitin-like PHD and RING finger domain-containing protein 2 (EC 6.3.2.-).
AL833522 - Homo sapiens mRNA; cDNA DKFZp686G0837 (from clone DKFZp686G0837).
JD492446 - Sequence 473470 from Patent EP1572962.
JD182309 - Sequence 163333 from Patent EP1572962.
JD382453 - Sequence 363477 from Patent EP1572962.
JD332784 - Sequence 313808 from Patent EP1572962.
AL137728 - Homo sapiens mRNA; cDNA DKFZp434B0920 (from clone DKFZp434B0920).
JD488867 - Sequence 469891 from Patent EP1572962.
JD044258 - Sequence 25282 from Patent EP1572962.
JD308091 - Sequence 289115 from Patent EP1572962.
JD339896 - Sequence 320920 from Patent EP1572962.
JD508979 - Sequence 490003 from Patent EP1572962.
JD525917 - Sequence 506941 from Patent EP1572962.
JD519803 - Sequence 500827 from Patent EP1572962.
JD368323 - Sequence 349347 from Patent EP1572962.
JD498660 - Sequence 479684 from Patent EP1572962.
JD133535 - Sequence 114559 from Patent EP1572962.
JD499471 - Sequence 480495 from Patent EP1572962.
JD433976 - Sequence 415000 from Patent EP1572962.
JD305656 - Sequence 286680 from Patent EP1572962.
JD353501 - Sequence 334525 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000276893.1, ENST00000276893.2, ENST00000276893.3, ENST00000276893.4, ENST00000276893.5, ENST00000276893.6, ENST00000276893.7, ENST00000276893.8, ENST00000276893.9, NIRF, NM_152896, Q5VYR1, Q5VYR3, Q659C8, Q8TAG7, Q96PU4, RNF107, uc317jlt.1, uc317jlt.2, UHRF2_HUMAN
UCSC ID: ENST00000276893.10_4
RefSeq Accession: NM_152896.3
Protein: Q96PU4 (aka UHRF2_HUMAN)

-  Gene Model Information
  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.