Dffb DNA fragmentation factor, beta subunit [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Dffbprovided by MGI
Official Full Name: DNA fragmentation factor, beta subunitprovided by MGI
Primary source: MGI:MGI:1196287
See related: Ensembl:ENSMUSG00000029027 AllianceGenome:MGI:1196287
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: CAD; CPAN; 40kDa; DFF40; Didff; 5730477D02Rik
Summary: Enables DNA binding activity and nuclease activity. Predicted to be involved in apoptotic DNA fragmentation; apoptotic chromosome condensation; and negative regulation of apoptotic DNA fragmentation. Predicted to be located in chromatin; cytosol; and nuclear lumen. Predicted to be part of protein-containing complex. Orthologous to human DFFB (DNA fragmentation factor subunit beta). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in thymus adult (RPKM 7.2), spleen adult (RPKM 5.4) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 E2; 4 83.78 cM

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (154048904..154059578, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (153964447..153975121, complement)

Chromosome 4 - NC_000070.7 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

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?

The Caspase-Activated DNase drives inflammation and contributes to defense against viral infection.
Title: The Caspase-Activated DNase drives inflammation and contributes to defense against viral infection.
Cell-free DNA in blood circulation is generated by DNase1L3 and caspase-activated DNase.
Title: Cell-free DNA in blood circulation is generated by DNase1L3 and caspase-activated DNase.
Dff40 expression is upregulated in atherosclerotic plaque. Dff40 deficiency inhibited high-fat diet-induced atherosclerosis, as evidenced by decreased atherosclerotic plaques, inhibited inflammatory response, and macrophage apoptosis, as well as enhanced stability of plaques.
Title: Loss of Caspase-Activated DNase Protects Against Atherosclerosis in Apolipoprotein E-Deficient Mice.
the highest order of chromatin compaction observed in the later steps of caspase-dependent apoptosis relies on DFF40/CAD-mediated DNA damage by generating 3'-OH ends in single-strand rather than double-strand DNA nicks/breaks
Title: Chromatin collapse during caspase-dependent apoptotic cell death requires DNA fragmentation factor, 40-kDa subunit-/caspase-activated deoxyribonuclease-mediated 3'-OH single-strand DNA breaks.
results show that caspase 3/CAD promotes cell differentiation by directly modifying the DNA/nuclear microenvironment, which enhances the expression of critical regulatory genes
Title: Caspase 3/caspase-activated DNase promote cell differentiation by inducing DNA strand breaks.
A los of caspase-activated DNASE enhances tumorigenesis induced by a chemical carcinogen in a model of skin carcinogenesis in mice.
Title: Increased skin carcinogenesis in caspase-activated DNase knockout mice.
The results suggest that CAD protein may be preferentially degraded by the ubiquitin-proteasome system in the absence of its inhibitor (ICAD) to maintain protein quality control.
Title: Degradation of caspase-activated DNase by the ubiquitin-proteasome system.
In transfected HeLa cells, transiently expressed DFF associates with chromatin, suggesting that DFF could be activated during apoptosis in a DNA-bound state
Title: Interaction of DNA fragmentation factor (DFF) with DNA reveals an unprecedented mechanism for nuclease inhibition and suggests that DFF can be activated in a DNA-bound state.
Interactions identified here between mouse liver histone H1 carboxyl-terminal domain and DFF40/CAD target and activate linker DNA cleavage during the terminal stages of apoptosis.
Title: The histone H1 C-terminal domain binds to the apoptotic nuclease, DNA fragmentation factor (DFF40/CAD) and stimulates DNA cleavage.
The thymus of DNase II(-/-)CAD(-/-) embryos contained many foci carrying undigested DNA and the cellularity was severely reduced due to a block in T cell development.
Title: Impaired thymic development in mouse embryos deficient in apoptotic DNA degradation.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Variation

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Alleles

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

Endonuclease-mediated (5)
Gene trapped (1)
Targeted (1) 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 DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA endonuclease activity	IEA Inferred from Electronic Annotation more info
enables DNA nuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA nuclease activity	ISO Inferred from Sequence Orthology more info
enables disordered domain specific binding	IEA Inferred from Electronic Annotation more info
enables disordered domain specific binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	IEA Inferred from Electronic Annotation more info
enables enzyme binding	ISO Inferred from Sequence Orthology 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 nuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in apoptotic DNA fragmentation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within apoptotic DNA fragmentation	ISO Inferred from Sequence Orthology more info	PubMed
involved_in apoptotic DNA fragmentation	ISO Inferred from Sequence Orthology more info
involved_in apoptotic chromosome condensation	IEA Inferred from Electronic Annotation more info
involved_in apoptotic chromosome condensation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic DNA fragmentation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic DNA fragmentation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromatin	IEA Inferred from Electronic Annotation more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	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	ISO Inferred from Sequence Orthology more info	PubMed
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA fragmentation factor subunit beta

Names: DFF-40; DNA fragmentation factor 40 kDa subunit; DNA fragmentation factor, 40 kD, beta subunit; DNase inhibited by DNA fragmentation factor; caspase-activated DNase; caspase-activated deoxyribonuclease

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_007859.4 → NP_031885.3 DNA fragmentation factor subunit beta

See identical proteins and their annotated locations for NP_031885.3

Status: VALIDATED

Source sequence(s)

AB009377, AK077619, BC053052

Consensus CDS

CCDS19004.1

UniProtKB/Swiss-Prot

O54788

UniProtKB/TrEMBL

Q7TS81, Q8BP66

Related

ENSMUSP00000030893.3, ENSMUST00000030893.3

Conserved Domains (2) summary

cd06535
Location:7 → 83

CIDE_N_CAD; CIDE_N domain of CAD nuclease. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are ...

pfam09230
Location:103 → 324

DFF40; DNA fragmentation factor 40 kDa

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_000070.7 Reference GRCm39 C57BL/6J

Range

154048904..154059578 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011250184.3 → XP_011248486.1 DNA fragmentation factor subunit beta isoform X2

See identical proteins and their annotated locations for XP_011248486.1

Conserved Domains (1) summary

pfam09230
Location:37 → 214

DFF40; DNA fragmentation factor 40 kDa
XM_030253183.2 → XP_030109043.1 DNA fragmentation factor subunit beta isoform X2

Conserved Domains (1) summary

pfam09230
Location:37 → 214

DFF40; DNA fragmentation factor 40 kDa
XM_036163646.1 → XP_036019539.1 DNA fragmentation factor subunit beta isoform X2

Conserved Domains (1) summary

pfam09230
Location:37 → 214

DFF40; DNA fragmentation factor 40 kDa
XM_011250183.4 → XP_011248485.1 DNA fragmentation factor subunit beta isoform X2

See identical proteins and their annotated locations for XP_011248485.1

Conserved Domains (1) summary

pfam09230
Location:37 → 214

DFF40; DNA fragmentation factor 40 kDa
XM_006538517.2 → XP_006538580.1 DNA fragmentation factor subunit beta isoform X1

Conserved Domains (2) summary

cd06535
Location:7 → 83

CIDE_N_CAD; CIDE_N domain of CAD nuclease. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are ...

pfam09230
Location:103 → 264

DFF40; DNA fragmentation factor 40 kDa