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DFFB DNA fragmentation factor subunit beta [ Homo sapiens (human) ]

Gene ID: 1677, updated on 12-Jan-2019

Summary

Official Symbol
DFFBprovided by HGNC
Official Full Name
DNA fragmentation factor subunit betaprovided by HGNC
Primary source
HGNC:HGNC:2773
See related
Ensembl:ENSG00000169598 MIM:601883
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CAD; CPAN; DFF2; DFF40; DFF-40
Summary
Apoptosis is a cell death process that removes toxic and/or useless cells during mammalian development. The apoptotic process is accompanied by shrinkage and fragmentation of the cells and nuclei and degradation of the chromosomal DNA into nucleosomal units. DNA fragmentation factor (DFF) is a heterodimeric protein of 40-kD (DFFB) and 45-kD (DFFA) subunits. DFFA is the substrate for caspase-3 and triggers DNA fragmentation during apoptosis. DFF becomes activated when DFFA is cleaved by caspase-3. The cleaved fragments of DFFA dissociate from DFFB, the active component of DFF. DFFB has been found to trigger both DNA fragmentation and chromatin condensation during apoptosis. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene but the biological validity of some of these variants has not been determined. [provided by RefSeq, Sep 2013]
Expression
Ubiquitous expression in duodenum (RPKM 1.4), spleen (RPKM 1.3) and 25 other tissues See more
Orthologs

Genomic context

See DFFB in Genome Data Viewer
Location:
1p36.32
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (3857267..3885429)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (3773845..3801993)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 574, pseudogene Neighboring gene leucine rich repeat containing 47 Neighboring gene centrosomal protein 104 Neighboring gene uncharacterized LOC107984910 Neighboring gene chromosome 1 open reading frame 174

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study identifies loci affecting blood copper, selenium and zinc.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
retropepsin gag-pol HIV-1 protease directly cleaves and activates procaspase 8 in T cells, which is associated with cleavage of BID, mitochondrial release of cytochrome c, activation of the downstream caspases 9 and 3, and cleavage of DFF and PARP PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Activation of DNA fragmentation factor, organism-specific biosystem (from REACTOME)
    Activation of DNA fragmentation factor, organism-specific biosystemDNA fragmentation in response to apoptotic signals is achieved, in part, through the activity of apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) (reviewed ...
  • Apoptosis, organism-specific biosystem (from KEGG)
    Apoptosis, organism-specific biosystemApoptosis is a genetically programmed process for the elimination of damaged or redundant cells by activation of caspases (aspartate-specific cysteine proteases). The onset of apoptosis is controlled...
  • Apoptosis, organism-specific biosystem (from WikiPathways)
    Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
  • Apoptosis, conserved biosystem (from KEGG)
    Apoptosis, conserved biosystemApoptosis is a genetically programmed process for the elimination of damaged or redundant cells by activation of caspases (aspartate-specific cysteine proteases). The onset of apoptosis is controlled...
  • Apoptosis, organism-specific biosystem (from REACTOME)
    Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
  • Apoptosis Modulation and Signaling, organism-specific biosystem (from WikiPathways)
    Apoptosis Modulation and Signaling, organism-specific biosystemApoptosis, or cell death program, can be activated by various mechanisms within the extrinsic and the intrinsic pathway. While activation of cell death receptors leads to the engagement of the extrin...
  • Apoptosis induced DNA fragmentation, organism-specific biosystem (from REACTOME)
    Apoptosis induced DNA fragmentation, organism-specific biosystemDNA fragmentation in response to apoptotic signals is achieved through the activity of two apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease...
  • Apoptotic execution phase, organism-specific biosystem (from REACTOME)
    Apoptotic execution phase, organism-specific biosystemIn the execution phase of apoptosis, effector caspases cleave vital cellular proteins leading to the morphological changes that characterize apoptosis. These changes include destruction of the nucle...
  • Caspase cascade in apoptosis, organism-specific biosystem (from Pathway Interaction Database)
    Caspase cascade in apoptosis, organism-specific biosystem
    Caspase cascade in apoptosis
  • Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation, organism-specific biosystem (from WikiPathways)
    Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation, organism-specific biosystemThis pathway describes the Fas induced apoptosis and interplay with Hsp27 in response to stress. More info: [http://www.biocarta.com/pathfiles/h_hsp27Pathway.asp BioCarta].
  • HIV-1 Nef: Negative effector of Fas and TNF-alpha, organism-specific biosystem (from Pathway Interaction Database)
    HIV-1 Nef: Negative effector of Fas and TNF-alpha, organism-specific biosystem
    HIV-1 Nef: Negative effector of Fas and TNF-alpha
  • Integrated Pancreatic Cancer Pathway, organism-specific biosystem (from WikiPathways)
    Integrated Pancreatic Cancer Pathway, organism-specific biosystemAn integrated pathway model which displays the protein-protein interactions (PPIs) among the relevant proteins for pancreatic cancer. This pathway is a collection of different mechanistic protein pat...
  • Programmed Cell Death, organism-specific biosystem (from REACTOME)
    Programmed Cell Death, organism-specific biosystemCell death is a fundamental cellular response that has a crucial role in shaping our bodies during development and in regulating tissue homeostasis by eliminating unwanted cells. There are a number o...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
deoxyribonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
deoxyribonuclease activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
disordered domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
identical protein binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
apoptotic DNA fragmentation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apoptotic DNA fragmentation IDA
Inferred from Direct Assay
more info
PubMed 
apoptotic DNA fragmentation TAS
Traceable Author Statement
more info
 
apoptotic chromosome condensation IDA
Inferred from Direct Assay
more info
PubMed 
protein homooligomerization IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
nuclear chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
DNA fragmentation factor subunit beta
Names
DNA fragmentation factor 40 kDa subunit
DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase)
caspase-activated DNase
caspase-activated deoxyribonuclease
caspase-activated nuclease

NCBI Reference Sequences (RefSeq)

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_001282669.1NP_001269598.1  DNA fragmentation factor subunit beta isoform 1

    See identical proteins and their annotated locations for NP_001269598.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AK303065, AL691523, BC032827, DC368011
    Consensus CDS
    CCDS72693.1
    UniProtKB/TrEMBL
    B4DZS0, Q96P73
    Related
    ENSP00000339524.4, ENST00000338895.7
    Conserved Domains (2) summary
    cd06535
    Location:480
    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:124347
    DFF40; DNA fragmentation factor 40 kDa
  2. NM_001320132.1NP_001307061.1  DNA fragmentation factor subunit beta isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and uses an alternate start codon, compared to variant 1. It encodes isoform 4, which has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AB028912, AF409060, AK027141, BC032827, DC368011
    UniProtKB/Swiss-Prot
    O76075
    UniProtKB/TrEMBL
    Q96P73, Q96P74
    Conserved Domains (1) summary
    pfam09230
    Location:51274
    DFF40; DNA fragmentation factor 40 kDa
  3. NM_001320136.1NP_001307065.1  DNA fragmentation factor subunit beta isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstrean in-frame start codon, compared to variant 1. It encodes isoform 5, which is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AF409062, AK027141, BC032827, DC368011
    UniProtKB/TrEMBL
    Q96P72, Q96P73
    Conserved Domains (1) summary
    pfam09230
    Location:36259
    DFF40; DNA fragmentation factor 40 kDa
  4. NM_004402.3NP_004393.1  DNA fragmentation factor subunit beta isoform 2

    See identical proteins and their annotated locations for NP_004393.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains two consecutive alternate splice junctions compared to variant 1. The resulting isoform (2) has the same N- and C-termini but lacks an internal segment compared to isoform 1.
    Source sequence(s)
    AL691523, BC032827, BC048797, DC368011
    Consensus CDS
    CCDS52.1
    UniProtKB/Swiss-Prot
    O76075
    UniProtKB/TrEMBL
    Q96P73
    Related
    ENSP00000367454.3, ENST00000378209.7
    Conserved Domains (2) summary
    cd06535
    Location:480
    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:100323
    DFF40; DNA fragmentation factor 40 kDa

RNA

  1. NR_104222.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice junction and contains an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL691523, BC032827, DC368011
    Related
    ENST00000468793.5
  2. NR_135150.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses alternate splice sites in two internal exons and contains an additional internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB028911, AF409060, AK027141, AL691523, BC032827, DC368011
    Related
    ENST00000491998.5
  3. NR_135151.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) uses alternate splice sites in two internal exons and contains an additional internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB028913, AF409060, AK027141, BC032827, CN275847, DC368011
    Related
    ENST00000477548.5
  4. NR_135152.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF409061, AK027141, BC032827, DC368011
    Related
    ENST00000475969.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    3857267..3885429
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000498.2XP_016855987.1  DNA fragmentation factor subunit beta isoform X1

  2. XM_017000499.1XP_016855988.1  DNA fragmentation factor subunit beta isoform X2

  3. XM_011540865.2XP_011539167.1  DNA fragmentation factor subunit beta isoform X4

    Conserved Domains (2) summary
    cd06535
    Location:480
    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:124168
    DFF40; DNA fragmentation factor 40 kDa
  4. XM_017000500.1XP_016855989.1  DNA fragmentation factor subunit beta isoform X3

RNA

  1. XR_946563.2 RNA Sequence

  2. XR_002959574.1 RNA Sequence

  3. XR_946565.1 RNA Sequence

  4. XR_001737013.1 RNA Sequence

  5. XR_001737011.2 RNA Sequence

  6. XR_001737012.2 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001004285.1: Suppressed sequence

    Description
    NM_001004285.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
  2. NM_001004286.1: Suppressed sequence

    Description
    NM_001004286.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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