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

    Gene ID: 1677, updated on 9-Dec-2024

    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; AllianceGenome:HGNC:2773
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See DFFB in Genome Data Viewer
    Location:
    1p36.32
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (3857476..3885429)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (3369074..3397333)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (3774040..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 NANOG-H3K27ac hESC enhancer GRCh37_chr1:3709930-3710608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 125 Neighboring gene Sharpr-MPRA regulatory region 1968 Neighboring gene centrosomal protein 104 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3745882-3747081 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:3747165-3748364 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:3755401-3755900 Neighboring gene uncharacterized LOC124903829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3767162-3767662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 67 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 127 Neighboring gene Sharpr-MPRA regulatory region 4254 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:3787529-3787731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 128 Neighboring gene chromosome 1 open reading frame 174 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:3815928-3816498 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:3816499-3817067 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:3817068-3817637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 130 Neighboring gene long intergenic non-protein coding RNA 1134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 131 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3827787-3828672

    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 Functions

    What's a GeneRIF?

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables disordered domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex 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)

    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_001282669.2NP_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
      Consensus CDS
      CCDS72693.1
      UniProtKB/TrEMBL
      B4DZS0
      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_001320132.2NP_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
      UniProtKB/Swiss-Prot
      O76075
      UniProtKB/TrEMBL
      Q96P73, Q96P74
      Conserved Domains (1) summary
      pfam09230
      Location:51274
      DFF40; DNA fragmentation factor 40 kDa
    3. NM_001320136.2NP_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_004402.4NP_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
      Consensus CDS
      CCDS52.1
      UniProtKB/Swiss-Prot
      O60521, O76075, Q5SR22, Q9BYI4, Q9BYI5, Q9BYI6
      Related
      ENSP00000367454.4, ENST00000378209.8
      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_104222.2 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
      Related
      ENST00000468793.5
    2. NR_135150.2 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
      Related
      ENST00000491998.5
    3. NR_135151.2 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
      Related
      ENST00000477548.5
    4. NR_135152.2 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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      3857476..3885429
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

    2. XM_017000500.2XP_016855989.1  DNA fragmentation factor subunit beta isoform X3

    3. XM_017000498.3XP_016855987.1  DNA fragmentation factor subunit beta isoform X1

    4. XM_011540865.3XP_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

    RNA

    1. XR_946563.3 RNA Sequence

    2. XR_946565.2 RNA Sequence

    3. XR_002959574.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      3369074..3397333
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334793.1XP_054190768.1  DNA fragmentation factor subunit beta isoform X2

    2. XM_054334794.1XP_054190769.1  DNA fragmentation factor subunit beta isoform X3

    3. XM_054334792.1XP_054190767.1  DNA fragmentation factor subunit beta isoform X1

    4. XM_054334795.1XP_054190770.1  DNA fragmentation factor subunit beta isoform X4

    RNA

    1. XR_008485941.1 RNA Sequence

    2. XR_008485943.1 RNA Sequence

    3. XR_008485942.1 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.