Uhrf1 ubiquitin-like with PHD and ring finger domains 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Uhrf1provided by RGD
Official Full Name: ubiquitin-like with PHD and ring finger domains 1provided by RGD
Primary source: RGD:1595855
See related: EnsemblRapid:ENSRNOG00000048411 AllianceGenome:RGD:1595855
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Np95; Ac2-121
Summary: Predicted to enable several functions, including DNA binding activity; histone H3 ubiquitin ligase activity; and zinc ion binding activity. Involved in response to peptide hormone. Predicted to be located in chromosome and nuclear lumen. Orthologous to human UHRF1 (ubiquitin like with PHD and ring finger domains 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 529.9), Spleen (RPKM 177.6) and 2 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q11

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (1220162..1241792)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (1133117..1154639)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (10738211..10758403, complement)

Chromosome 9 - NC_086027.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

UHRF1 inhibits the late phase of oligodendrocyte differentiation.
Title: Functional genomic analysis of oligodendrocyte differentiation.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables cis-regulatory region sequence-specific 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	IEA Inferred from Electronic Annotation more info
enables hemi-methylated DNA-binding	ISO Inferred from Sequence Orthology more info
enables hemi-methylated DNA-binding	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3 ubiquitin ligase activity	IEA Inferred from Electronic Annotation more info
enables histone H3 ubiquitin ligase activity	ISO Inferred from Sequence Orthology more info
enables histone binding	IEA Inferred from Electronic Annotation more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methyl-CpG binding	IEA Inferred from Electronic Annotation more info
enables methyl-CpG binding	ISO Inferred from Sequence Orthology more info
enables methylated histone binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	ISO Inferred from Sequence Orthology more info
enables methylated histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables nucleic acid binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IEA Inferred from Electronic Annotation more info
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 ubiquitin-protein transferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin formation	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin formation	ISO Inferred from Sequence Orthology more info
involved_in heterochromatin formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in mitotic spindle assembly	IEA Inferred from Electronic Annotation more info
involved_in mitotic spindle assembly	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression via chromosomal CpG island methylation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression via chromosomal CpG island methylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein metabolic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein metabolic process	ISO Inferred from Sequence Orthology more info
involved_in protein autoubiquitination	IEA Inferred from Electronic Annotation 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 protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in regulation of epithelial cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in regulation of epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in response to peptide hormone	IEP Inferred from Expression Pattern more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in chromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in euchromatin	IEA Inferred from Electronic Annotation more info
located_in euchromatin	ISO Inferred from Sequence Orthology more info
located_in euchromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in heterochromatin	IEA Inferred from Electronic Annotation more info
located_in heterochromatin	ISO Inferred from Sequence Orthology more info
located_in heterochromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear matrix	IEA Inferred from Electronic Annotation more info
located_in nuclear matrix	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in replication fork	IEA Inferred from Electronic Annotation more info
located_in replication fork	ISO Inferred from Sequence Orthology more info
located_in replication fork	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase UHRF1

Names: RING-type E3 ubiquitin transferase UHRF1; liver regeneration-related protein LRRG126; nuclear protein 95; ubiquitin-like PHD and RING finger domain-containing protein 1; ubiquitin-like, containing PHD and RING finger domains, 1; ubiquitin-like-containing PHD and RING finger domains protein 1

NP_001380773.1

EC 2.3.2.27

NP_001380774.1

EC 2.3.2.27

NP_001380775.1

EC 2.3.2.27

XP_038939390.1

EC 2.3.2.27

XP_063123131.1

EC 2.3.2.27

XP_063123132.1

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_001393844.2 → NP_001380773.1 E3 ubiquitin-protein ligase UHRF1 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/TrEMBL

A0A0G2JT07, A0A0G2JXJ2

Conserved Domains (5) summary

cd15525
Location:322 → 368

PHD_UHRF1_2; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2

cd16613
Location:711 → 755

RING-HC_UHRF; RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins

cd17122
Location:1 → 74

Ubl_UHRF1; ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 1(UHRF1)

pfam02182
Location:422 → 588

SAD_SRA; SAD/SRA domain

pfam12148
Location:129 → 280

TTD; Tandem tudor domain within UHRF1
NM_001393845.2 → NP_001380774.1 E3 ubiquitin-protein ligase UHRF1 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/TrEMBL

A0A0G2JT07, A0A0G2JXJ2

Conserved Domains (5) summary

cd15525
Location:322 → 368

PHD_UHRF1_2; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2

cd16613
Location:711 → 755

RING-HC_UHRF; RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins

cd17122
Location:1 → 74

Ubl_UHRF1; ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 1(UHRF1)

pfam02182
Location:422 → 588

SAD_SRA; SAD/SRA domain

pfam12148
Location:129 → 280

TTD; Tandem tudor domain within UHRF1
NM_001393846.2 → NP_001380775.1 E3 ubiquitin-protein ligase UHRF1 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/Swiss-Prot

Q4FZR4, Q7TPK1

UniProtKB/TrEMBL

A0A0G2JT07

Related

ENSRNOP00000066794.1, ENSRNOT00000075265.4

Conserved Domains (5) summary

cd15525
Location:314 → 360

PHD_UHRF1_2; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2

cd16613
Location:703 → 747

RING-HC_UHRF; RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins

cd17122
Location:1 → 74

Ubl_UHRF1; ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 1(UHRF1)

pfam02182
Location:414 → 580

SAD_SRA; SAD/SRA domain

pfam12148
Location:129 → 280

TTD; Tandem tudor domain within UHRF1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086027.1 Reference GRCr8

Range

1220162..1241792

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039083462.2 → XP_038939390.1 E3 ubiquitin-protein ligase UHRF1 isoform X1

UniProtKB/TrEMBL

A0A0G2JT07, A0A0G2JXJ2

Related

ENSRNOP00000109975.1, ENSRNOT00000170673.1

Conserved Domains (5) summary

cd15525
Location:322 → 368

PHD_UHRF1_2; PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2

cd16613
Location:711 → 755

RING-HC_UHRF; RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins

cd17122
Location:1 → 74

Ubl_UHRF1; ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 1(UHRF1)

pfam02182
Location:422 → 588

SAD_SRA; SAD/SRA domain

pfam12148
Location:129 → 280

TTD; Tandem tudor domain within UHRF1
XM_063267061.1 → XP_063123131.1 E3 ubiquitin-protein ligase UHRF1 isoform X2

UniProtKB/Swiss-Prot

Q4FZR4, Q7TPK1

UniProtKB/TrEMBL

A0A0G2JT07

Related

ENSRNOP00000070294.2, ENSRNOT00000083848.3
XM_063267062.1 → XP_063123132.1 E3 ubiquitin-protein ligase UHRF1 isoform X2

UniProtKB/Swiss-Prot

Q4FZR4, Q7TPK1

UniProtKB/TrEMBL

A0A0G2JT07

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001008882.1: Suppressed sequence

Description

NM_001008882.1: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.