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

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; AllianceGenome:HGNC:12556
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: mouse all
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Genomic context

Location:: 19p13.3

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (4903080..4962154)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (4888314..4947375)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (4903092..4962165)

Chromosome 19 - NC_000019.10 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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells.
Title: CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells.
Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells.
Title: Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells.
NLRP14 deficiency causes female infertility with oocyte maturation defects and early embryonic arrest by impairing cytoplasmic UHRF1 abundance.
Title: NLRP14 deficiency causes female infertility with oocyte maturation defects and early embryonic arrest by impairing cytoplasmic UHRF1 abundance.
RNF106 aggravates esophageal squamous cell carcinoma progression through LATS2/YAP axis.
Title: RNF106 aggravates esophageal squamous cell carcinoma progression through LATS2/YAP axis.
UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma.
Title: UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma.
Interfering with the Expression of Ubiquitin-Like with PHD and Ring Finger Domains 1 Can Inhibit the Invasion of Human Renal Cell Carcinoma.
Title: Interfering with the Expression of Ubiquitin-Like with PHD and Ring Finger Domains 1 Can Inhibit the Invasion of Human Renal Cell Carcinoma.
UHRF1 promotes spindle assembly and chromosome congression by catalyzing EG5 polyubiquitination.
Title: UHRF1 promotes spindle assembly and chromosome congression by catalyzing EG5 polyubiquitination.
Refined read-out: The hUHRF1 Tandem-Tudor domain prefers binding to histone H3 tails containing K4me1 in the context of H3K9me2/3.
Title: Refined read-out: The hUHRF1 Tandem-Tudor domain prefers binding to histone H3 tails containing K4me1 in the context of H3K9me2/3.
The UHRF1 protein is a key regulator of retrotransposable elements and innate immune response to viral RNA in human cells.
Title: The UHRF1 protein is a key regulator of retrotransposable elements and innate immune response to viral RNA in human cells.
Lenvatinib inhibited HCC cell migration and invasion through regulating the transcription and ubiquitination of UHRF1 and DNMT1.
Title: Lenvatinib inhibited HCC cell migration and invasion through regulating the transcription and ubiquitination of UHRF1 and DNMT1.

Submit: New GeneRIF Correction See all GeneRIFs (191)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

RH26361 (e-PCR)
- UniSTS:90369

D11S3374 (e-PCR)
- UniSTS:152616

RH36905 (e-PCR)
- UniSTS:87932

D19S216 (e-PCR), detects polymorphism
- UniSTS:51853

D19S216 (e-PCR), detects polymorphism
- UniSTS:69061

G22294 (e-PCR)
- UniSTS:67554

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA damage sensor activity	TAS Traceable Author Statement more info	PubMed
enables H3K9me3 modified histone binding	TAS Traceable Author Statement more info	PubMed
enables cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables hemi-methylated DNA-binding	IDA Inferred from Direct Assay more info	PubMed
enables hemi-methylated DNA-binding	TAS Traceable Author Statement more info	PubMed
enables histone H3 ubiquitin ligase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone binding	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	ISS Inferred from Sequence or Structural Similarity more info
enables methyl-CpG binding	IDA Inferred from Direct Assay more info	PubMed
enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleic acid binding	EXP Inferred from Experiment more info	PubMed
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 ligase activity	ISS Inferred from Sequence or Structural Similarity more info
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage response	TAS Traceable Author Statement more info	PubMed
involved_in double-strand break repair via homologous recombination	TAS Traceable Author Statement more info	PubMed
involved_in epigenetic regulation of gene expression	TAS Traceable Author Statement more info	PubMed
involved_in heterochromatin formation	IDA Inferred from Direct Assay more info	PubMed
involved_in homologous recombination	TAS Traceable Author Statement more info	PubMed
involved_in mitotic spindle assembly	IDA Inferred from Direct Assay 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 negative regulation of gene expression via chromosomal CpG island methylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity	IC Inferred by Curator more info	PubMed
involved_in positive regulation of protein metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IC Inferred by Curator more info	PubMed
involved_in protein autoubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of epithelial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	ISS Inferred from Sequence or Structural Similarity more info
part_of euchromatin	IDA Inferred from Direct Assay more info	PubMed
part_of heterochromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear matrix	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in replication fork	IDA Inferred from Direct Assay more info	PubMed
is_active_in spindle	IC Inferred by Curator more info	PubMed

General protein information

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Preferred Names: E3 ubiquitin-protein ligase UHRF1

Names: RING finger protein 106; RING-type E3 ubiquitin transferase UHRF1; inverted CCAAT box binding protein 90; 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

EC 2.3.2.27

NP_001276979.1

EC 2.3.2.27

NP_001276980.1

EC 2.3.2.27

NP_001276981.1

EC 2.3.2.27

NP_037414.3

EC 2.3.2.27

XP_011526244.1

EC 2.3.2.27

XP_047294663.1

EC 2.3.2.27

XP_047294664.1

EC 2.3.2.27

XP_047294665.1

EC 2.3.2.27

XP_054176730.1

EC 2.3.2.27

XP_054176731.1

EC 2.3.2.27

XP_054176732.1

EC 2.3.2.27

XP_054176733.1

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.

Genomic

NG_033256.2 RefSeqGene

Range

11422..64075

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001048201.3 → NP_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

A0JBR2, A8K024, B2RBA9, Q2HIX7, Q8J022, Q96T88, Q9H6S6, Q9P115, Q9P1U7

UniProtKB/TrEMBL

A0A087WTW0

Related

ENSP00000498698.1, ENST00000650932.1

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:724 → 766

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:317 → 363

PHD_UHRF1; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1)

pfam02182
Location:417 → 584

SAD_SRA; SAD/SRA domain

pfam12148
Location:133 → 284

TTD; Tandem tudor domain within UHRF1
NM_001290050.2 → NP_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

A0JBR2, A8K024, B2RBA9, Q2HIX7, Q8J022, Q96T88, Q9H6S6, Q9P115, Q9P1U7

UniProtKB/TrEMBL

A0A087WTW0

Related

ENSP00000484739.1, ENST00000612630.4

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:724 → 766

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:317 → 363

PHD_UHRF1; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1)

pfam02182
Location:417 → 584

SAD_SRA; SAD/SRA domain

pfam12148
Location:133 → 284

TTD; Tandem tudor domain within UHRF1
NM_001290051.2 → NP_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

A0JBR2, A8K024, B2RBA9, Q2HIX7, Q8J022, Q96T88, Q9H6S6, Q9P115, Q9P1U7

UniProtKB/TrEMBL

A0A087WTW0

Related

ENSP00000478601.1, ENST00000615884.4

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:724 → 766

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:317 → 363

PHD_UHRF1; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1)

pfam02182
Location:417 → 584

SAD_SRA; SAD/SRA domain

pfam12148
Location:133 → 284

TTD; Tandem tudor domain within UHRF1
NM_001290052.2 → NP_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

A0JBR2, A8K024, B2RBA9, Q2HIX7, Q8J022, Q96T88, Q9H6S6, Q9P115, Q9P1U7

UniProtKB/TrEMBL

A0A087WTW0

Related

ENSP00000478348.1, ENST00000616255.1

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:724 → 766

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:317 → 363

PHD_UHRF1; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1)

pfam02182
Location:417 → 584

SAD_SRA; SAD/SRA domain

pfam12148
Location:133 → 284

TTD; Tandem tudor domain within UHRF1
NM_013282.5 → NP_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/TrEMBL

A0A087WTW0, A0A087WVR3

Related

ENSP00000479617.1, ENST00000622802.4

Conserved Domains (6) summary

cd01797
Location:14 → 91

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

smart00213
Location:16 → 87

UBQ; Ubiquitin homologues

cd00162
Location:737 → 779

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:330 → 376

PHD_UHRF1; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1)

pfam02182
Location:430 → 597

SAD_SRA; SAD/SRA domain

pfam12148
Location:146 → 297

TTD; Tandem tudor domain within UHRF1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

4903080..4962154

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A087WTW0

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:689 → 731

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:317 → 363

PHD_UHRF1; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1)

pfam02182
Location:417 → 549

SAD_SRA; SAD/SRA domain

pfam12148
Location:133 → 284

TTD; Tandem tudor domain within UHRF1
XM_047438707.1 → XP_047294663.1 E3 ubiquitin-protein ligase UHRF1 isoform X1
XM_047438708.1 → XP_047294664.1 E3 ubiquitin-protein ligase UHRF1 isoform X2
XM_047438709.1 → XP_047294665.1 E3 ubiquitin-protein ligase UHRF1 isoform X1