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

Gene ID: 231600, updated on 8-Feb-2024

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 cellular protein metabolic process; positive regulation of cellular protein metabolic process; and protein destabilization. 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, Apr 2022]
Expression
Ubiquitous expression in thymus adult (RPKM 17.7), CNS E14 (RPKM 15.6) and 28 other tissues See more
Orthologs
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Genomic context

See Chfr in Genome Data Viewer
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_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E4778 Neighboring gene STARR-positive B cell enhancer ABC_E10339 Neighboring gene STARR-positive B cell enhancer ABC_E3597 Neighboring gene phosphatidylinositol-specific phospholipase C, X domain containing 1 Neighboring gene GTP binding protein 6 (putative) Neighboring gene zinc finger protein 605 Neighboring gene STARR-positive B cell enhancer ABC_E6362 Neighboring gene nucleophosmin pseudogene Neighboring gene STARR-seq mESC enhancer starr_13946 Neighboring gene STARR-positive B cell enhancer mm9_chr5:110605377-110605678 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:110605669-110605852 Neighboring gene predicted gene 15787 Neighboring gene golgin A3 Neighboring gene uncharacterized LOC118568795 Neighboring gene STARR-seq mESC enhancer starr_13947 Neighboring gene ankyrin repeat and LEM domain containing 2

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 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 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
acts_upstream_of_or_within cell cycle IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cell division 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 ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in mitotic cell cycle checkpoint signaling IBA
Inferred from Biological aspect of Ancestor
more info
 
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 protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
 
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
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
E3 ubiquitin-protein ligase CHFR
Names
RING-type E3 ubiquitin transferase CHFR
NP_001276506.1
NP_001276507.1
NP_001276508.1
NP_001276509.1
NP_766305.2
XP_011247747.1
XP_011247748.1
XP_030110278.1
XP_030110279.1
XP_030110280.1
XP_036020978.1
XP_036020979.1
XP_036020980.1
XP_036020981.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001289577.1NP_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:27140
    FHA; Forkhead associated (FHA) domain, binds pSer, pThr, pTyr [Signal transduction mechanisms]
    cd00060
    Location:16105
    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:302345
    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 ...
  2. NM_001289578.1NP_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:27103
    FHA; Forkhead associated (FHA) domain, binds pSer, pThr, pTyr [Signal transduction mechanisms]
    cd00060
    Location:16105
    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:230273
    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 ...
  3. NM_001289579.1NP_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:139362
    rad18; DNA repair protein rad18
    cd16503
    Location:159202
    RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)
    pfam17979
    Location:326480
    zf-CRD; Cysteine rich domain with multizinc binding regions
  4. NM_001289580.1NP_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:139361
    rad18; DNA repair protein rad18
    cd16503
    Location:159202
    RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)
    pfam17979
    Location:326479
    zf-CRD; Cysteine rich domain with multizinc binding regions
  5. NM_172717.4NP_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:27140
    FHA; Forkhead associated (FHA) domain, binds pSer, pThr, pTyr [Signal transduction mechanisms]
    cd00060
    Location:16105
    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:302345
    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

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    110283599..110319839
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (3) summary
    TIGR00599
    Location:139361
    rad18; DNA repair protein rad18
    cd16503
    Location:159202
    RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)
    pfam17979
    Location:326479
    zf-CRD; Cysteine rich domain with multizinc binding regions
  2. XM_011249445.3XP_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:139362
    rad18; DNA repair protein rad18
    cd16503
    Location:159202
    RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)
    pfam17979
    Location:326480
    zf-CRD; Cysteine rich domain with multizinc binding regions
  3. XM_011249446.3XP_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:139362
    rad18; DNA repair protein rad18
    cd16503
    Location:159202
    RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)
    pfam17979
    Location:326480
    zf-CRD; Cysteine rich domain with multizinc binding regions
  4. XM_036165087.1XP_036020980.1  E3 ubiquitin-protein ligase CHFR isoform X3

    Conserved Domains (3) summary
    TIGR00599
    Location:139361
    rad18; DNA repair protein rad18
    cd16503
    Location:159202
    RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)
    pfam17979
    Location:326479
    zf-CRD; Cysteine rich domain with multizinc binding regions
  5. XM_030254419.2XP_030110279.1  E3 ubiquitin-protein ligase CHFR isoform X3

    Conserved Domains (3) summary
    TIGR00599
    Location:139361
    rad18; DNA repair protein rad18
    cd16503
    Location:159202
    RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)
    pfam17979
    Location:326479
    zf-CRD; Cysteine rich domain with multizinc binding regions
  6. XM_036165085.1XP_036020978.1  E3 ubiquitin-protein ligase CHFR isoform X1

    Conserved Domains (4) summary
    cd00060
    Location:558
    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:232455
    rad18; DNA repair protein rad18
    cd16503
    Location:252295
    RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)
    pfam17979
    Location:419573
    zf-CRD; Cysteine rich domain with multizinc binding regions
  7. XM_030254420.2XP_030110280.1  E3 ubiquitin-protein ligase CHFR isoform X4

    Conserved Domains (3) summary
    TIGR00599
    Location:1206
    rad18; DNA repair protein rad18
    cd16503
    Location:346
    RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)
    pfam17979
    Location:170324
    zf-CRD; Cysteine rich domain with multizinc binding regions
  8. XM_036165088.1XP_036020981.1  E3 ubiquitin-protein ligase CHFR isoform X4

    Conserved Domains (3) summary
    TIGR00599
    Location:1206
    rad18; DNA repair protein rad18
    cd16503
    Location:346
    RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)
    pfam17979
    Location:170324
    zf-CRD; Cysteine rich domain with multizinc binding regions
  9. XM_036165086.1XP_036020979.1  E3 ubiquitin-protein ligase CHFR isoform X2

    Conserved Domains (3) summary
    TIGR00599
    Location:139362
    rad18; DNA repair protein rad18
    cd16503
    Location:159202
    RING-HC_CHFR; RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR)
    pfam17979
    Location:326480
    zf-CRD; Cysteine rich domain with multizinc binding regions

RNA

  1. XR_001784679.2 RNA Sequence

    Related
    ENSMUST00000198066.5
  2. XR_004942506.1 RNA Sequence