UHRF2 ubiquitin like with PHD and ring finger domains 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: UHRF2provided by HGNC
Official Full Name: ubiquitin like with PHD and ring finger domains 2provided by HGNC
Primary source: HGNC:HGNC:12557
See related: Ensembl:ENSG00000147854 MIM:615211; AllianceGenome:HGNC:12557
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NIRF; URF2; RNF107; TDRD23
Summary: This gene encodes a nuclear protein which is involved in cell-cycle regulation. The encoded protein is a ubiquitin-ligase capable of ubiquinating PCNP (PEST-containing nuclear protein), and together they may play a role in tumorigenesis. The encoded protein contains an NIRF_N domain, a PHD finger, a set- and ring-associated (SRA) domain, and a RING finger domain and several of these domains have been shown to be essential for the regulation of cell proliferation. This protein may also have a role in intranuclear degradation of polyglutamine aggregates. Alternative splicing results in multiple transcript variants some of which are non-protein coding. [provided by RefSeq, Feb 2012]
Expression: Ubiquitous expression in bone marrow (RPKM 16.7), lymph node (RPKM 12.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9p24.1

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (6413199..6507054)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (6418255..6512105)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (6413199..6507054)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

MiR-196a promotes the proliferation and migration of esophageal cancer via the UHRF2/TET2 axis.
Title: MiR-196a promotes the proliferation and migration of esophageal cancer via the UHRF2/TET2 axis.
UHRF2 promotes Hepatocellular Carcinoma Progression by Upregulating ErbB3/Ras/Raf Signaling Pathway.
Title: UHRF2 promotes Hepatocellular Carcinoma Progression by Upregulating ErbB3/Ras/Raf Signaling Pathway.
IGF2BP1/UHRF2 Axis Mediated by miR-98-5p to Promote the Proliferation of and Inhibit the Apoptosis of Esophageal Squamous Cell Carcinoma.
Title: IGF2BP1/UHRF2 Axis Mediated by miR-98-5p to Promote the Proliferation of and Inhibit the Apoptosis of Esophageal Squamous Cell Carcinoma.
HBx promotes hepatocarcinogenesis by enhancing phosphorylation and blocking ubiquitinylation of UHRF2.
Title: HBx promotes hepatocarcinogenesis by enhancing phosphorylation and blocking ubiquitinylation of UHRF2.
UHRF2 commissions the completion of DNA demethylation through allosteric activation by 5hmC and K33-linked ubiquitination of XRCC1.
Title: UHRF2 commissions the completion of DNA demethylation through allosteric activation by 5hmC and K33-linked ubiquitination of XRCC1.
UV-induced activation of ATR is mediated by UHRF2.
Title: UV-induced activation of ATR is mediated by UHRF2.
UHRF2 promotes intestinal tumorigenesis through stabilization of TCF4 mediated Wnt/beta-catenin signaling.
Title: UHRF2 promotes intestinal tumorigenesis through stabilization of TCF4 mediated Wnt/β-catenin signaling.
Uncoupling of UHRF2 from the DNA methylation maintenance program is linked to differences in the molecular readout of chromatin signatures that connect UHRF1 to ubiquitination of histone H3.
Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance.
Immunoprecipitation and immunofluorescence staining reveled that UHRF2 combined with p21 in the nucleus. In addition, UHRF2 degraded p21 through ubiquitination and shortened the half-life of p21.
Title: UHRF2 promotes DNA damage response by decreasing p21 via RING finger domain.
UHRF2 may be a negative regulator of EMT and a novel prognostic biomarker for ESCC.
Title: Identification of UHRF2 as a Negative Regulator of Epithelial-Mesenchymal Transition and Its Clinical Significance in Esophageal Squamous Cell Carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (35)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of periodontal pathogen colonization. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D9S1629 (e-PCR)
- UniSTS:153621

RH45850 (e-PCR)
- UniSTS:26142

SHGC-53467 (e-PCR)
- UniSTS:19614

RH36184 (e-PCR)
- UniSTS:65439

A008T41 (e-PCR)
- UniSTS:27571

WI-14338 (e-PCR)
- UniSTS:2294

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables SUMO transferase activity	EXP Inferred from Experiment more info	PubMed
enables histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein autoubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein sumoylation	TAS Traceable Author Statement more info
involved_in protein ubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of cell cycle	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of cell cycle	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in heterochromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in pericentric heterochromatin	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: E3 ubiquitin-protein ligase UHRF2

Names: Np95-like ring finger protein; RING finger protein 107; RING-type E3 ubiquitin transferase UHRF2; np95/ICBP90-like RING finger protein; nuclear protein 97; nuclear zinc finger protein NP97; ubiquitin-like PHD and RING finger domain-containing protein 2; ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase; ubiquitin-like, containing PHD and RING finger domains, 2; ubiquitin-like-containing PHD and RING finger domains protein 2

NP_690856.1

EC 2.3.2.27

XP_011516006.1

EC 2.3.2.27

XP_011516007.1

EC 2.3.2.27

XP_016869742.1

EC 2.3.2.27

XP_047278704.1

EC 2.3.2.27

XP_047278705.1

EC 2.3.2.27

XP_054217917.1

EC 2.3.2.27

XP_054217918.1

EC 2.3.2.27

XP_054217919.1

EC 2.3.2.27

XP_054217920.1

EC 2.3.2.27

XP_054217921.1

EC 2.3.2.27

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_152896.3 → NP_690856.1 E3 ubiquitin-protein ligase UHRF2

See identical proteins and their annotated locations for NP_690856.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the shorter transcript.

Source sequence(s)

AB071698, AF274049, BG709183

Consensus CDS

CCDS6469.1

UniProtKB/Swiss-Prot

Q5VYR1, Q5VYR3, Q659C8, Q8TAG7, Q96PU4

Related

ENSP00000276893.5, ENST00000276893.10

Conserved Domains (6) summary

cd01797
Location:1 → 78

NIRF_N; amino-terminal ubiquitin-like domain of Np95 and NIRF

smart00213
Location:3 → 74

UBQ; Ubiquitin homologues

cd00162
Location:732 → 775

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd15617
Location:346 → 392

PHD_UHRF2; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2)

pfam02182
Location:446 → 614

SAD_SRA; SAD/SRA domain

pfam12148
Location:125 → 312

TTD; Tandem tudor domain within UHRF1

RNA

NR_046386.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an alternate internal exon in the coding region, compared to variant 1, which results in a frameshift and early stop codon. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB071698, AF274049, BC028397

Related

ENST00000468435.7

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

6413199..6507054

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017014253.2 → XP_016869742.1 E3 ubiquitin-protein ligase UHRF2 isoform X1
XM_047422748.1 → XP_047278704.1 E3 ubiquitin-protein ligase UHRF2 isoform X2
XM_011517704.3 → XP_011516006.1 E3 ubiquitin-protein ligase UHRF2 isoform X3

See identical proteins and their annotated locations for XP_011516006.1

Conserved Domains (4) summary

cd00162
Location:509 → 552

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd15617
Location:123 → 169

PHD_UHRF2; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2)

pfam02182
Location:223 → 391

SAD_SRA; SAD/SRA domain

pfam12148
Location:1 → 89

TTD; Tandem tudor domain within UHRF1
XM_011517705.3 → XP_011516007.1 E3 ubiquitin-protein ligase UHRF2 isoform X3

See identical proteins and their annotated locations for XP_011516007.1

Conserved Domains (4) summary

cd00162
Location:509 → 552

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd15617
Location:123 → 169

PHD_UHRF2; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2)

pfam02182
Location:223 → 391

SAD_SRA; SAD/SRA domain

pfam12148
Location:1 → 89

TTD; Tandem tudor domain within UHRF1
XM_047422749.1 → XP_047278705.1 E3 ubiquitin-protein ligase UHRF2 isoform X4

RNA

XR_428418.5 RNA Sequence
XR_007061241.1 RNA Sequence
XR_007061242.1 RNA Sequence
XR_007061243.1 RNA Sequence
XR_007061244.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

6418255..6512105

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054361942.1 → XP_054217917.1 E3 ubiquitin-protein ligase UHRF2 isoform X1
XM_054361943.1 → XP_054217918.1 E3 ubiquitin-protein ligase UHRF2 isoform X2
XM_054361944.1 → XP_054217919.1 E3 ubiquitin-protein ligase UHRF2 isoform X3
XM_054361945.1 → XP_054217920.1 E3 ubiquitin-protein ligase UHRF2 isoform X3
XM_054361946.1 → XP_054217921.1 E3 ubiquitin-protein ligase UHRF2 isoform X4

RNA

XR_008487935.1 RNA Sequence
XR_008487936.1 RNA Sequence
XR_008487937.1 RNA Sequence
XR_008487938.1 RNA Sequence
XR_008487939.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_152306.2: Suppressed sequence

Description

NM_152306.2: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.