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

    Gene ID: 84359, updated on 27-Nov-2024

    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
    NEW
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    Genomic context

    See Dffb in Genome Data Viewer
    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_086023.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102551503 Neighboring gene similar to human chromosome 1 open reading frame 174 Neighboring gene centrosomal protein 104 Neighboring gene leucine rich repeat containing 47 Neighboring gene small integral membrane protein 1 (Vel blood group)

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    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_053362.2NP_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:783
      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:103324
      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

    1. NC_086023.1 Reference GRCr8

      Range
      169804873..169817157 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063288500.1XP_063144570.1  DNA fragmentation factor subunit beta isoform X3

    2. XM_039110874.2XP_038966802.1  DNA fragmentation factor subunit beta isoform X1

      UniProtKB/TrEMBL
      A0A0H2UHU4, A6IUJ9
      Related
      ENSRNOP00000096977.2, ENSRNOT00000105778.2
      Conserved Domains (2) summary
      cd06535
      Location:27103
      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:124345
      DFF40; DNA fragmentation factor 40 kDa
    3. XM_063288499.1XP_063144569.1  DNA fragmentation factor subunit beta isoform X2

    RNA

    1. XR_005504541.2 RNA Sequence

    2. XR_005504543.2 RNA Sequence

    3. XR_005504544.2 RNA Sequence