uhrf1 ubiquitin-like with PHD and ring finger domains 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: uhrf1provided by ZNC
Official Full Name: ubiquitin-like with PHD and ring finger domains 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-2039
See related: Ensembl:ENSDARG00000103409 AllianceGenome:ZFIN:ZDB-GENE-040426-2039
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: NP95; fb97f09; unm_b1115; zgc:63539; wu:fb97f09
Summary: Predicted to enable several functions, including hemi-methylated DNA-binding activity; methylated histone binding activity; and zinc ion binding activity. Acts upstream of or within several processes, including intestinal epithelial structure maintenance; lens development in camera-type eye; and negative regulation of gene expression via chromosomal CpG island methylation. Is active in cytoplasm and nucleus. Is expressed in several structures, including brain; eye; liver; pleuroperitoneal region; and presumptive neural retina. Orthologous to human UHRF1 (ubiquitin like with PHD and ring finger domains 1). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 22

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	22	NC_007133.7 (4408643..4439311, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	22	NC_007133.6 (3955795..3986463, complement)

Chromosome 22 - NC_007133.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

uhrf1 and dnmt1 Loss Induces an Immune Response in Zebrafish Livers Due to Viral Mimicry by Transposable Elements.
Title: uhrf1 and dnmt1 Loss Induces an Immune Response in Zebrafish Livers Due to Viral Mimicry by Transposable Elements.
the role of Uhrf1 and Dnmt1 in the coordination of intestinal development
Title: Epigenetic factors Dnmt1 and Uhrf1 coordinate intestinal development.
Dnmt1 stability requires UHRF1 phosphorylation and that crosstalk between the proteins is essential for the function of these two important epigenetic regulators during gastrulation
Title: UHRF1 regulation of Dnmt1 is required for pre-gastrula zebrafish development.
DNA hypomethylation is the mechanism underlying the cell cycle block and small liver phenotype caused by uhrf1 depletion.
Title: DNA hypomethylation induces a DNA replication-associated cell cycle arrest to block hepatic outgrowth in uhrf1 mutant zebrafish embryos.
an essential role for UHRF1 phosphorylation by cyclin-dependent kinase 2/cyclin A2 during early vertebrate development
Title: UHRF1 phosphorylation by cyclin A2/cyclin-dependent kinase 2 is required for zebrafish embryogenesis.
These data provide the first evidence that Uhrf1 and Dnmt1 function is required for vertebrate lens development and maintenance.
Title: Uhrf1 and Dnmt1 are required for development and maintenance of the zebrafish lens.
uhrf1 is required for physiologic liver growth in both embryos and adults
Title: Liver growth in the embryo and during liver regeneration in zebrafish requires the cell cycle regulator, uhrf1.

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General gene information

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Markers

fb97f09.x1 (e-PCR)
- UniSTS:203595

fc86c12.y1 (e-PCR)
- UniSTS:194682

fb96c02.y1 (e-PCR)
- UniSTS:191902

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables hemi-methylated DNA-binding	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	ISS Inferred from Sequence or Structural Similarity more info
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 transferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within animal organ regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin formation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within inflammatory response	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within inflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within intestinal epithelial structure maintenance	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within intestinal epithelial structure maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lens development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within liver development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within liver development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of gene expression via chromosomal CpG island methylation	IMP Inferred from Mutant Phenotype more info	PubMed
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	ISS Inferred from Sequence or Structural Similarity 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 ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in chromatin	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in euchromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in heterochromatin	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation 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; 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; unm b1115

NP_998242.1

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_213077.1 → NP_998242.1 E3 ubiquitin-protein ligase UHRF1

See identical proteins and their annotated locations for NP_998242.1

Status: PROVISIONAL

Source sequence(s)

BC058055

UniProtKB/Swiss-Prot

E7EZF3, Q1LUQ1, Q6DRP6, Q6PEI0

Related

ENSDARP00000135054.1, ENSDART00000169317.2

Conserved Domains (6) summary

cd01797
Location:1 → 78

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

smart00184
Location:705 → 743

RING; Ring finger

smart00213
Location:3 → 74

UBQ; Ubiquitin homologues

cd15616
Location:314 → 360

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

pfam02182
Location:414 → 581

SAD_SRA; SAD/SRA domain

pfam12148
Location:135 → 278

TTD; Tandem tudor domain within UHRF1