Dffb DNA fragmentation factor subunit beta [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Dffbprovided by RGD
Official Full Name: DNA fragmentation factor subunit betaprovided by RGD
Primary source: RGD:620335
See related: EnsemblRapid:ENSRNOG00000025030 AllianceGenome:RGD:620335
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Cad
Summary: Enables DNA nuclease activity. Involved in apoptotic DNA fragmentation. Predicted to be located in chromatin; cytosol; and nuclear lumen. Predicted to be part of protein-containing complex. Biomarker of transient cerebral ischemia. Orthologous to human DFFB (DNA fragmentation factor subunit beta). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 36.2), Kidney (RPKM 35.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (169804873..169817157, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (164522446..164534733, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (171250559..171261875, complement)

Chromosome 5 - NC_086023.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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?

DNA fragmentation in neuronal apoptosis is catalyzed by either CAD or DNase gamma depending on the differentiation state
Title: Differential DNases are selectively used in neuronal apoptosis depending on the differentiation state.
Results suggest that Ebp1 contributes to inhibition of DNA fragmentation by caspase-activated DNase, and that nuclear Akt might contribute to suppressing apoptosis through interaction with Ebp1.
Title: Nuclear Akt associates with PKC-phosphorylated Ebp1, preventing DNA fragmentation by inhibition of caspase-activated DNase.
Data indicate increases in the nuclear levels of caspase-activated acinus and DNase and Endonuclease G (a caspase-independent endonuclease) in CA1 and CA3 pyramidal cell nuclei with different temporal patterns following an AMPA-insult.
Title: AMPA-induced excitotoxicity increases nuclear levels of CAD, endonuclease G, and acinus and induces chromatin condensation in rat hippocampal pyramidal neurons.
that variations in TP53 and hCAD genes modulate the age of onset of Huntington disease .
Title: Modulation of age at onset of Huntington disease patients by variations in TP53 and human caspase activated DNase (hCAD) genes.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

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 DNA binding	ISO Inferred from Sequence Orthology more info
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	IDA Inferred from Direct Assay more info	PubMed
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	ISO Inferred from Sequence Orthology more info
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
involved_in apoptotic DNA fragmentation	IDA Inferred from Direct Assay more info	PubMed
involved_in apoptotic DNA fragmentation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within apoptotic DNA fragmentation	ISO Inferred from Sequence Orthology more info
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 cytoplasm	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
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 polypeptide (caspase-activated DNase); DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase); DNA fragmentation factor, beta polypeptide (caspase-activated DNase); DNA fragmentation factor, beta subunit; 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_053362.2 → NP_445814.1 DNA fragmentation factor subunit beta

See identical proteins and their annotated locations for NP_445814.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000005

UniProtKB/Swiss-Prot

Q99N34

UniProtKB/TrEMBL

A0A8I6AS11

Related

ENSRNOP00000034722.4, ENSRNOT00000032825.7

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_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

169804873..169817157 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063288500.1 → XP_063144570.1 DNA fragmentation factor subunit beta isoform X3
XM_039110874.2 → XP_038966802.1 DNA fragmentation factor subunit beta isoform X1

UniProtKB/TrEMBL

A0A0H2UHU4, A6IUJ9

Related

ENSRNOP00000096977.2, ENSRNOT00000105778.2

Conserved Domains (2) summary

cd06535
Location:27 → 103

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:124 → 345

DFF40; DNA fragmentation factor 40 kDa
XM_063288499.1 → XP_063144569.1 DNA fragmentation factor subunit beta isoform X2