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UHRF1 ubiquitin like with PHD and ring finger domains 1 [ Homo sapiens (human) ]

Gene ID: 29128, updated on 23-Dec-2018

Summary

Official Symbol
UHRF1provided by HGNC
Official Full Name
ubiquitin like with PHD and ring finger domains 1provided by HGNC
Primary source
HGNC:HGNC:12556
See related
Ensembl:ENSG00000276043 MIM:607990
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
Np95; hNP95; ICBP90; RNF106; TDRD22; hUHRF1; huNp95
Summary
This gene encodes a member of a subfamily of RING-finger type E3 ubiquitin ligases. The protein binds to specific DNA sequences, and recruits a histone deacetylase to regulate gene expression. Its expression peaks at late G1 phase and continues during G2 and M phases of the cell cycle. It plays a major role in the G1/S transition by regulating topoisomerase IIalpha and retinoblastoma gene expression, and functions in the p53-dependent DNA damage checkpoint. It is regarded as a hub protein for the integration of epigenetic information. This gene is up-regulated in various cancers, and it is therefore considered to be a therapeutic target. Multiple transcript variants encoding different isoforms have been found for this gene. A related pseudogene exists on chromosome 12. [provided by RefSeq, Feb 2014]
Expression
Broad expression in bone marrow (RPKM 7.7), lymph node (RPKM 6.3) and 14 other tissues See more
Orthologs

Genomic context

See UHRF1 in Genome Data Viewer
Location:
19p13.3
Exon count:
20
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (4903080..4962154)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (4909510..4962165)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene toll like receptor adaptor molecule 1 Neighboring gene perilipin 3 Neighboring gene arrestin domain containing 5 Neighboring gene microRNA 4747 Neighboring gene lysine demethylase 4B Neighboring gene protein tyrosine phosphatase, receptor type S Neighboring gene ribosomal protein L32 pseudogene 34

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • DNA methylation, organism-specific biosystem (from REACTOME)
    DNA methylation, organism-specific biosystemMethylation of cytosine is catalyzed by a family of DNA methyltransferases (DNMTs): DNMT1, DNMT3A, and DNMT3B transfer methyl groups from S-adenosylmethionine to cytosine, producing 5-methylcytosine ...
  • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
    Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystem (from WikiPathways)
    Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystemProtein pathways altered by mutations in adenoid cystic carcinoma. Pathways include epigentic modification, DNA damage checkpoint signals, MYB/MYC signalling pathway, FGF/IGF/PI3K signalling, and not...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ21925, MGC138707

Gene Ontology Provided by GOA

Function Evidence Code Pubs
hemi-methylated DNA-binding IDA
Inferred from Direct Assay
more info
PubMed 
histone binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding ISS
Inferred from Sequence or Structural Similarity
more info
 
methyl-CpG binding IDA
Inferred from Direct Assay
more info
PubMed 
methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
nucleosomal histone binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin protein ligase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
DNA repair IEA
Inferred from Electronic Annotation
more info
 
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell proliferation IEP
Inferred from Expression Pattern
more info
PubMed 
histone monoubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone monoubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 
histone ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
maintenance of DNA methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
maintenance of DNA methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity IC
Inferred by Curator
more info
PubMed 
positive regulation of cellular protein metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IC
Inferred by Curator
more info
PubMed 
protein autoubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
euchromatin IDA
Inferred from Direct Assay
more info
PubMed 
heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear heterochromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear matrix ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
replication fork IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
E3 ubiquitin-protein ligase UHRF1
Names
RING finger protein 106
RING-type E3 ubiquitin transferase UHRF1
inverted CCAAT box-binding protein of 90 kDa
nuclear phosphoprotein 95
nuclear protein 95
nuclear zinc finger protein Np95
transcription factor ICBP90
ubiquitin-like PHD and RING finger domain-containing protein 1
NP_001041666.1
NP_001276979.1
NP_001276980.1
NP_001276981.1
NP_037414.3
XP_011526244.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_033256.2 RefSeqGene

    Range
    11351..64075
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001048201.3NP_001041666.1  E3 ubiquitin-protein ligase UHRF1 isoform 1

    See identical proteins and their annotated locations for NP_001041666.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the shorter isoform (1). Variants 1, 3, 4 and 5 all encode isoform 1.
    Source sequence(s)
    AC104525, AK025578, AK074377, AK289389, AK314579
    Consensus CDS
    CCDS74263.1
    UniProtKB/Swiss-Prot
    Q96T88
    Related
    ENSP00000485604.1, ENST00000624301.3
    Conserved Domains (6) summary
    cd01797
    Location:178
    NIRF_N; amino-terminal ubiquitin-like domain of Np95 and NIRF
    smart00213
    Location:374
    UBQ; Ubiquitin homologues
    cd00162
    Location:724766
    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 ...
    cd15616
    Location:317363
    PHD_UHRF1; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1)
    pfam02182
    Location:417584
    SAD_SRA; SAD/SRA domain
    pfam12148
    Location:133284
    TTD; Tandem tudor domain within UHRF1
  2. NM_001290050.1NP_001276979.1  E3 ubiquitin-protein ligase UHRF1 isoform 1

    See identical proteins and their annotated locations for NP_001276979.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1, 3, 4 and 5 all encode isoform 1.
    Source sequence(s)
    AB177623, AC027319, AC104525, AK025578
    Consensus CDS
    CCDS74263.1
    UniProtKB/Swiss-Prot
    Q96T88
    Related
    ENSP00000484739.1, ENST00000612630.4
    Conserved Domains (6) summary
    cd01797
    Location:178
    NIRF_N; amino-terminal ubiquitin-like domain of Np95 and NIRF
    smart00213
    Location:374
    UBQ; Ubiquitin homologues
    cd00162
    Location:724766
    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 ...
    cd15616
    Location:317363
    PHD_UHRF1; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1)
    pfam02182
    Location:417584
    SAD_SRA; SAD/SRA domain
    pfam12148
    Location:133284
    TTD; Tandem tudor domain within UHRF1
  3. NM_001290051.1NP_001276980.1  E3 ubiquitin-protein ligase UHRF1 isoform 1

    See identical proteins and their annotated locations for NP_001276980.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, compared to variant 1. Variants 1, 3, 4 and 5 all encode isoform 1.
    Source sequence(s)
    AC027319, AC104525, AK025578, AK289389, HY074450, KF459704
    Consensus CDS
    CCDS74263.1
    UniProtKB/Swiss-Prot
    Q96T88
    Related
    ENSP00000478601.1, ENST00000615884.4
    Conserved Domains (6) summary
    cd01797
    Location:178
    NIRF_N; amino-terminal ubiquitin-like domain of Np95 and NIRF
    smart00213
    Location:374
    UBQ; Ubiquitin homologues
    cd00162
    Location:724766
    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 ...
    cd15616
    Location:317363
    PHD_UHRF1; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1)
    pfam02182
    Location:417584
    SAD_SRA; SAD/SRA domain
    pfam12148
    Location:133284
    TTD; Tandem tudor domain within UHRF1
  4. NM_001290052.1NP_001276981.1  E3 ubiquitin-protein ligase UHRF1 isoform 1

    See identical proteins and their annotated locations for NP_001276981.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 1. Variants 1, 3, 4 and 5 all encode isoform 1.
    Source sequence(s)
    AB177624, AC027319, AC104525, AK025578, EF560733
    Consensus CDS
    CCDS74263.1
    UniProtKB/Swiss-Prot
    Q96T88
    Related
    ENSP00000478348.1, ENST00000616255.1
    Conserved Domains (6) summary
    cd01797
    Location:178
    NIRF_N; amino-terminal ubiquitin-like domain of Np95 and NIRF
    smart00213
    Location:374
    UBQ; Ubiquitin homologues
    cd00162
    Location:724766
    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 ...
    cd15616
    Location:317363
    PHD_UHRF1; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1)
    pfam02182
    Location:417584
    SAD_SRA; SAD/SRA domain
    pfam12148
    Location:133284
    TTD; Tandem tudor domain within UHRF1
  5. NM_013282.4NP_037414.3  E3 ubiquitin-protein ligase UHRF1 isoform 2

    See identical proteins and their annotated locations for NP_037414.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and initiates translation from an alternate start codon, compared to variant 1. The resulting isoform (2) has a distinct N-terminus and is longer than isoform 1.
    Source sequence(s)
    AB177624, AC104525, AK025578, AK074377, BC113875
    Consensus CDS
    CCDS74262.1
    UniProtKB/Swiss-Prot
    Q96T88
    UniProtKB/TrEMBL
    A0A087WVR3
    Related
    ENSP00000479617.1, ENST00000622802.4
    Conserved Domains (6) summary
    cd01797
    Location:1491
    NIRF_N; amino-terminal ubiquitin-like domain of Np95 and NIRF
    smart00213
    Location:1687
    UBQ; Ubiquitin homologues
    cd00162
    Location:737779
    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 ...
    cd15616
    Location:330376
    PHD_UHRF1; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1)
    pfam02182
    Location:430597
    SAD_SRA; SAD/SRA domain
    pfam12148
    Location:146297
    TTD; Tandem tudor domain within UHRF1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    4903080..4962154
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011527942.2XP_011526244.1  E3 ubiquitin-protein ligase UHRF1 isoform X1

    Conserved Domains (6) summary
    cd01797
    Location:178
    NIRF_N; amino-terminal ubiquitin-like domain of Np95 and NIRF
    smart00213
    Location:374
    UBQ; Ubiquitin homologues
    cd00162
    Location:689731
    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 ...
    cd15616
    Location:317363
    PHD_UHRF1; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1)
    pfam02182
    Location:417549
    SAD_SRA; SAD/SRA domain
    pfam12148
    Location:133284
    TTD; Tandem tudor domain within UHRF1
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