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Uhrf1 ubiquitin-like, containing PHD and RING finger domains, 1 [ Mus musculus (house mouse) ]

Gene ID: 18140, updated on 12-Mar-2024

Summary

Official Symbol
Uhrf1provided by MGI
Official Full Name
ubiquitin-like, containing PHD and RING finger domains, 1provided by MGI
Primary source
MGI:MGI:1338889
See related
Ensembl:ENSMUSG00000001228 AllianceGenome:MGI:1338889
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Np95; ICBP90; RNF106
Summary
Enables several functions, including hemi-methylated DNA-binding activity; histone binding activity; and ubiquitin protein ligase activity. Involved in maintenance of DNA methylation; negative regulation of transcription by RNA polymerase II; and protein ubiquitination. Located in heterochromatin; nuclear matrix; and replication fork. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; hindlimb phalanx; and sensory organ. Orthologous to human UHRF1 (ubiquitin like with PHD and ring finger domains 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in thymus adult (RPKM 54.8), liver E14 (RPKM 50.8) and 17 other tissues See more
Orthologs
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Genomic context

See Uhrf1 in Genome Data Viewer
Location:
17 D; 17 29.26 cM
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (56610405..56630486)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (56303337..56323486)

Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E8686 Neighboring gene STARR-positive B cell enhancer ABC_E3207 Neighboring gene perilipin 3 Neighboring gene STARR-positive B cell enhancer ABC_E3208 Neighboring gene STARR-positive B cell enhancer ABC_E3209 Neighboring gene arrestin domain containing 5 Neighboring gene STARR-positive B cell enhancer ABC_E141 Neighboring gene lysine (K)-specific demethylase 4B Neighboring gene STARR-positive B cell enhancer ABC_E8923 Neighboring gene predicted gene, 32715 Neighboring gene protein tyrosine phosphatase receptor type S Neighboring gene microRNA 6977

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Gene trapped (2) 
  • Targeted (5)  1 citation
  • Chemically induced (ENU) (1)  1 citation
  • Endonuclease-mediated (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables hemi-methylated DNA-binding IDA
Inferred from Direct Assay
more info
PubMed 
enables hemi-methylated DNA-binding ISO
Inferred from Sequence Orthology
more info
 
enables histone H3 ubiquitin ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables histone binding ISO
Inferred from Sequence Orthology
more info
 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables methyl-CpG binding ISO
Inferred from Sequence Orthology
more info
 
enables methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables methylated histone binding ISO
Inferred from Sequence Orthology
more info
 
enables nucleic acid binding ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
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 ligase activity ISO
Inferred from Sequence Orthology
more info
 
enables ubiquitin-protein transferase activity ISO
Inferred from Sequence Orthology
more info
 
enables zinc ion binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within DNA damage response IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within DNA repair IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cell cycle IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in heterochromatin formation ISO
Inferred from Sequence Orthology
more info
 
involved_in mitotic spindle assembly ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of gene expression via CpG island methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of gene expression via CpG island methylation ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of protein metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in protein autoubiquitination ISO
Inferred from Sequence Orthology
more info
 
involved_in protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of epithelial cell proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in ubiquitin-dependent protein catabolic process ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
PubMed 
part_of chromatin ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
part_of euchromatin ISO
Inferred from Sequence Orthology
more info
 
part_of heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
part_of heterochromatin ISO
Inferred from Sequence Orthology
more info
 
located_in nuclear matrix IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus TAS
Traceable Author Statement
more info
PubMed 
located_in replication fork IDA
Inferred from Direct Assay
more info
PubMed 
located_in replication fork ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
E3 ubiquitin-protein ligase UHRF1
Names
RING-type E3 ubiquitin transferase UHRF1
mUhrf1
nuclear protein 95
nuclear zinc finger protein Np95
ubiquitin-like PHD and RING finger domain-containing protein 1
ubiquitin-like-containing PHD and RING finger domains protein 1
NP_001104548.1
NP_001104549.1
NP_001104550.1
NP_001400286.1
NP_001400287.1
NP_001400288.1
NP_001400289.1
NP_035061.3

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)

  1. NM_001111078.2NP_001104548.1  E3 ubiquitin-protein ligase UHRF1 isoform A

    See identical proteins and their annotated locations for NP_001104548.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode isoform (A).
    Source sequence(s)
    AC026385
    Consensus CDS
    CCDS28903.1
    UniProtKB/Swiss-Prot
    Q3U9D7, Q3U9P2, Q3UI74, Q3UIE6, Q3ULF2, Q3ULQ0, Q8C6F1, Q8VDF2, Q8VIA1, Q9Z1H6
    Related
    ENSMUSP00000108662.3, ENSMUST00000113039.9
    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:713755
    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 ...
    cd15525
    Location:322368
    PHD_UHRF1_2; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2
    pfam02182
    Location:422588
    SAD_SRA; SAD/SRA domain
    pfam12148
    Location:129281
    TTD; Tandem tudor domain within UHRF1
  2. NM_001111079.2NP_001104549.1  E3 ubiquitin-protein ligase UHRF1 isoform B

    See identical proteins and their annotated locations for NP_001104549.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the coding region, compared to variant 1, resulting in a shorter protein (isoform B). Variants 3 and 4 encode isoform B.
    Source sequence(s)
    AC026385
    Consensus CDS
    CCDS50151.1
    UniProtKB/Swiss-Prot
    Q8VDF2
    Related
    ENSMUSP00000108661.2, ENSMUST00000113038.8
    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:705747
    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 ...
    cd15525
    Location:314360
    PHD_UHRF1_2; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2
    pfam02182
    Location:414580
    SAD_SRA; SAD/SRA domain
    pfam12148
    Location:129281
    TTD; Tandem tudor domain within UHRF1
  3. NM_001111080.2NP_001104550.1  E3 ubiquitin-protein ligase UHRF1 isoform B

    See identical proteins and their annotated locations for NP_001104550.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the coding region and differs in the 5' UTR, compared to variant 1, resulting in a shorter protein (isoform B). Variants 3 and 4 encode isoform B.
    Source sequence(s)
    AC026385
    Consensus CDS
    CCDS50151.1
    UniProtKB/Swiss-Prot
    Q8VDF2
    Related
    ENSMUSP00000108658.2, ENSMUST00000113035.8
    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:705747
    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 ...
    cd15525
    Location:314360
    PHD_UHRF1_2; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2
    pfam02182
    Location:414580
    SAD_SRA; SAD/SRA domain
    pfam12148
    Location:129281
    TTD; Tandem tudor domain within UHRF1
  4. NM_001413357.1NP_001400286.1  E3 ubiquitin-protein ligase UHRF1 isoform C

    Status: VALIDATED

    Source sequence(s)
    AC026385
  5. NM_001413358.1NP_001400287.1  E3 ubiquitin-protein ligase UHRF1 isoform D

    Status: VALIDATED

    Source sequence(s)
    AC026385
  6. NM_001413359.1NP_001400288.1  E3 ubiquitin-protein ligase UHRF1 isoform E

    Status: VALIDATED

    Source sequence(s)
    AC026385
  7. NM_001413360.1NP_001400289.1  E3 ubiquitin-protein ligase UHRF1 isoform D

    Status: VALIDATED

    Source sequence(s)
    AC026385
  8. NM_010931.4NP_035061.3  E3 ubiquitin-protein ligase UHRF1 isoform A

    See identical proteins and their annotated locations for NP_035061.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (A). Variants 1 and 2 encode isoform (A).
    Source sequence(s)
    AC026385
    Consensus CDS
    CCDS28903.1
    UniProtKB/Swiss-Prot
    Q3U9D7, Q3U9P2, Q3UI74, Q3UIE6, Q3ULF2, Q3ULQ0, Q8C6F1, Q8VDF2, Q8VIA1, Q9Z1H6
    Related
    ENSMUSP00000001258.9, ENSMUST00000001258.15
    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:713755
    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 ...
    cd15525
    Location:322368
    PHD_UHRF1_2; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2
    pfam02182
    Location:422588
    SAD_SRA; SAD/SRA domain
    pfam12148
    Location:129281
    TTD; Tandem tudor domain within UHRF1

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000083.7 Reference GRCm39 C57BL/6J

    Range
    56610405..56630486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)