Chfr checkpoint with forkhead and ring finger domains [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Chfrprovided by MGI
Official Full Name: checkpoint with forkhead and ring finger domainsprovided by MGI
Primary source: MGI:MGI:2444898
See related: Ensembl:ENSMUSG00000014668 AllianceGenome:MGI:2444898
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: RNF116; C230082M18; 5730484M20Rik
Summary: Enables ubiquitin protein ligase activity. Acts upstream of or within several processes, including positive regulation of protein metabolic process; protein destabilization; and protein polyubiquitination. Predicted to be located in PML body. Predicted to be active in nucleus. Is expressed in embryo. Orthologous to human CHFR (checkpoint with forkhead and ring finger domains). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in thymus adult (RPKM 17.7), CNS E14 (RPKM 15.6) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 5 F; 5 53.32 cM

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	5	NC_000071.7 (110283599..110319839)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	5	NC_000071.6 (110135755..110171973)

Chromosome 5 - NC_000071.7 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ubiquitin ligase CHFR mediated degradation of VE-cadherin through ubiquitylation disrupts endothelial adherens junctions.
Title: Ubiquitin ligase CHFR mediated degradation of VE-cadherin through ubiquitylation disrupts endothelial adherens junctions.
CHFR is important for the survival of male premeiotic germ cells, which is likely through maintaining genomic stability in spermatogonial stem cells.
Title: CHFR is important for the survival of male premeiotic germ cells.
The interaction between CHFR and PARP-1 plays an important role in cell cycle regulation and cancer therapeutic strategies.
Title: CHFR protein regulates mitotic checkpoint by targeting PARP-1 protein for ubiquitination and degradation.
CHFR interacts with BRG1, SNF5, and BAF60a of the SWI/SNF-like BAF complex and ubiquitinates them to target for degradation through a proteasome-mediated pathway; SRG3 stabilizes these components by blocking their interaction with CHFR.
Title: SRG3/mBAF155 stabilizes the SWI/SNF-like BAF complex by blocking CHFR mediated ubiquitination and degradation of its major components.
RNF8 and Chfr, function together to activate ATM and maintain genomic stability in vivo.
Title: Chfr and RNF8 synergistically regulate ATM activation.
Stil protein regulates centrosome integrity and mitosis through suppression of Chfr.
Title: The Stil protein regulates centrosome integrity and mitosis through suppression of Chfr.
Mice with deficiencies in both Chfr and Mlh1 (the gene that encodes the DNA mismatch-repair protein Mlh1) displayed dramatically higher incidence of spontaneous tumors relative to mice deficient for only one of these genes.
Title: Deficiencies in Chfr and Mlh1 synergistically enhance tumor susceptibility in mice.
PML bodies control the distribution, dynamics and function of CHFR
Title: PML bodies control the nuclear dynamics and function of the CHFR mitotic checkpoint protein.
Downregulation of Chfr contributes to tumorigenesis by controlling the expression levels of Aurora A.
Title: Chfr is required for tumor suppression and Aurora A regulation.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	ISO Inferred from Sequence Orthology more info
enables nucleotide binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables ubiquitin-protein transferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin-protein transferase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in meiotic spindle checkpoint signaling	IEA Inferred from Electronic Annotation more info
involved_in meiotic spindle checkpoint signaling	ISO Inferred from Sequence Orthology more info
involved_in mitotic G2/M transition checkpoint	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitotic G2/M transition checkpoint	ISO Inferred from Sequence Orthology more info
involved_in mitotic G2/M transition checkpoint	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within mitotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of proteasomal ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within protein destabilization	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within protein polyubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in PML body	ISO Inferred from Sequence Orthology more info
located_in PML body	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase CHFR

Names: RING-type E3 ubiquitin transferase CHFR

NP_001276506.1

EC 2.3.2.27

NP_001276507.1

EC 2.3.2.27

NP_001276508.1

EC 2.3.2.27

NP_001276509.1

EC 2.3.2.27

NP_766305.2

EC 2.3.2.27

XP_011247747.1

EC 2.3.2.27

XP_011247748.1

EC 2.3.2.27

XP_030110278.1

EC 2.3.2.27

XP_030110279.1

EC 2.3.2.27

XP_030110280.1

EC 2.3.2.27

XP_036020978.1

EC 2.3.2.27

XP_036020979.1

EC 2.3.2.27

XP_036020980.1

EC 2.3.2.27

XP_036020981.1

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_001289577.1 → NP_001276506.1 E3 ubiquitin-protein ligase CHFR isoform 1

See identical proteins and their annotated locations for NP_001276506.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC118260

Consensus CDS

CCDS71637.1

UniProtKB/Swiss-Prot

Q3TFD8, Q3U233, Q3U4U9, Q3UGJ9, Q810L3, Q8BJZ9, Q8BWH4

Related

ENSMUSP00000108138.3, ENSMUST00000112519.9

Conserved Domains (3) summary

COG1716
Location:27 → 140

FHA; Forkhead associated (FHA) domain, binds pSer, pThr, pTyr [Signal transduction mechanisms]

cd00060
Location:16 → 105

FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...

cd00162
Location:302 → 345

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 ...
NM_001289578.1 → NP_001276507.1 E3 ubiquitin-protein ligase CHFR isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.

Source sequence(s)

AC118260, AK147892

Consensus CDS

CCDS80358.1

UniProtKB/Swiss-Prot

Q810L3

Related

ENSMUSP00000143480.2, ENSMUST00000198633.5

Conserved Domains (3) summary

COG1716
Location:27 → 103

FHA; Forkhead associated (FHA) domain, binds pSer, pThr, pTyr [Signal transduction mechanisms]

cd00060
Location:16 → 105

FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...

cd00162
Location:230 → 273

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 ...
NM_001289579.1 → NP_001276508.1 E3 ubiquitin-protein ligase CHFR isoform 4

See identical proteins and their annotated locations for NP_001276508.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) contains an alternate exon in the 5' region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus than isoform 1.

Source sequence(s)

AC118260, AK169182

UniProtKB/Swiss-Prot

Q810L3

Conserved Domains (3) summary

TIGR00599
Location:139 → 362

rad18; DNA repair protein rad18

cd16503
Location:159 → 202

RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)

pfam17979
Location:326 → 480

zf-CRD; Cysteine rich domain with multizinc binding regions
NM_001289580.1 → NP_001276509.1 E3 ubiquitin-protein ligase CHFR isoform 5

See identical proteins and their annotated locations for NP_001276509.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) contains an alternate exon in the 5' region, uses an alternate in-frame splice site, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.

Source sequence(s)

AC118260, AK048930, AK169182

UniProtKB/Swiss-Prot

Q810L3

Conserved Domains (3) summary

TIGR00599
Location:139 → 361

rad18; DNA repair protein rad18

cd16503
Location:159 → 202

RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)

pfam17979
Location:326 → 479

zf-CRD; Cysteine rich domain with multizinc binding regions
NM_172717.4 → NP_766305.2 E3 ubiquitin-protein ligase CHFR isoform 2

See identical proteins and their annotated locations for NP_766305.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC118260, AK077629

Consensus CDS

CCDS19522.1

UniProtKB/Swiss-Prot

Q810L3

Related

ENSMUSP00000014812.9, ENSMUST00000014812.13

Conserved Domains (3) summary

COG1716
Location:27 → 140

FHA; Forkhead associated (FHA) domain, binds pSer, pThr, pTyr [Signal transduction mechanisms]

cd00060
Location:16 → 105

FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...

cd00162
Location:302 → 345

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 ...

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

NC_000071.7 Reference GRCm39 C57BL/6J

Range

110283599..110319839

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030254418.2 → XP_030110278.1 E3 ubiquitin-protein ligase CHFR isoform X3

Conserved Domains (3) summary

TIGR00599
Location:139 → 361

rad18; DNA repair protein rad18

cd16503
Location:159 → 202

RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)

pfam17979
Location:326 → 479

zf-CRD; Cysteine rich domain with multizinc binding regions
XM_011249445.3 → XP_011247747.1 E3 ubiquitin-protein ligase CHFR isoform X2

See identical proteins and their annotated locations for XP_011247747.1

UniProtKB/Swiss-Prot

Q810L3

Conserved Domains (3) summary

TIGR00599
Location:139 → 362

rad18; DNA repair protein rad18

cd16503
Location:159 → 202

RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)

pfam17979
Location:326 → 480

zf-CRD; Cysteine rich domain with multizinc binding regions
XM_011249446.3 → XP_011247748.1 E3 ubiquitin-protein ligase CHFR isoform X2

See identical proteins and their annotated locations for XP_011247748.1

UniProtKB/Swiss-Prot

Q810L3

Conserved Domains (3) summary

TIGR00599
Location:139 → 362

rad18; DNA repair protein rad18

cd16503
Location:159 → 202

RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)

pfam17979
Location:326 → 480

zf-CRD; Cysteine rich domain with multizinc binding regions
XM_036165087.1 → XP_036020980.1 E3 ubiquitin-protein ligase CHFR isoform X3

Conserved Domains (3) summary

TIGR00599
Location:139 → 361

rad18; DNA repair protein rad18

cd16503
Location:159 → 202

RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)

pfam17979
Location:326 → 479

zf-CRD; Cysteine rich domain with multizinc binding regions
XM_030254419.2 → XP_030110279.1 E3 ubiquitin-protein ligase CHFR isoform X3

Conserved Domains (3) summary

TIGR00599
Location:139 → 361

rad18; DNA repair protein rad18

cd16503
Location:159 → 202

RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)

pfam17979
Location:326 → 479

zf-CRD; Cysteine rich domain with multizinc binding regions
XM_036165085.1 → XP_036020978.1 E3 ubiquitin-protein ligase CHFR isoform X1

Conserved Domains (4) summary

cd00060
Location:5 → 58

FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...

TIGR00599
Location:232 → 455

rad18; DNA repair protein rad18

cd16503
Location:252 → 295

RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)

pfam17979
Location:419 → 573

zf-CRD; Cysteine rich domain with multizinc binding regions
XM_030254420.2 → XP_030110280.1 E3 ubiquitin-protein ligase CHFR isoform X4

Conserved Domains (3) summary

TIGR00599
Location:1 → 206

rad18; DNA repair protein rad18

cd16503
Location:3 → 46

RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)

pfam17979
Location:170 → 324

zf-CRD; Cysteine rich domain with multizinc binding regions
XM_036165088.1 → XP_036020981.1 E3 ubiquitin-protein ligase CHFR isoform X4

Conserved Domains (3) summary

TIGR00599
Location:1 → 206

rad18; DNA repair protein rad18

cd16503
Location:3 → 46

RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)

pfam17979
Location:170 → 324

zf-CRD; Cysteine rich domain with multizinc binding regions
XM_036165086.1 → XP_036020979.1 E3 ubiquitin-protein ligase CHFR isoform X2

Conserved Domains (3) summary

TIGR00599
Location:139 → 362

rad18; DNA repair protein rad18

cd16503
Location:159 → 202

RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)

pfam17979
Location:326 → 480

zf-CRD; Cysteine rich domain with multizinc binding regions