Human Gene DFFB (uc001alc.3)
  Description: Homo sapiens DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase) (DFFB), mRNA.
RefSeq Summary (NM_004402): 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].
Transcript (Including UTRs)
   Position: hg19 chr1:3,773,845-3,801,993 Size: 28,149 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr1:3,774,168-3,800,305 Size: 26,138 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:3,773,845-3,801,993)mRNA (may differ from genome)Protein (338 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DFFB_HUMAN
DESCRIPTION: RecName: Full=DNA fragmentation factor subunit beta; EC=3.-.-.-; AltName: Full=Caspase-activated deoxyribonuclease; Short=CAD; Short=Caspase-activated DNase; AltName: Full=Caspase-activated nuclease; Short=CPAN; AltName: Full=DNA fragmentation factor 40 kDa subunit; Short=DFF-40;
FUNCTION: Nuclease that induces DNA fragmentation and chromatin condensation during apoptosis. Degrades naked DNA and induces apoptotic morphology.
ENZYME REGULATION: Inhibited by DFFA (DFF45).
SUBUNIT: Heterodimer of DFFA and DFFB. Interacts with HIST1H1A.
INTERACTION: O00273:DFFA; NbExp=1; IntAct=EBI-1053821, EBI-727171;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
SIMILARITY: Contains 1 CIDE-N domain.

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DFFB
CDC HuGE Published Literature: DFFB

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.98 RPKM in Brain - Cerebellum
Total median expression: 150.52 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -153.40323-0.475 Picture PostScript Text
3' UTR -583.081688-0.345 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015311 - Apoptosis_DFF40
IPR003508 - CAD

Pfam Domains:
PF02017 - CIDE-N domain
PF09230 - DNA fragmentation factor 40 kDa

SCOP Domains:
54277 - CAD & PB1 domains
54060 - His-Me finger endonucleases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1IBX - NMR


ModBase Predicted Comparative 3D Structure on O76075
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004518 nuclease activity
GO:0004536 deoxyribonuclease activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0019899 enzyme binding
GO:0019904 protein domain specific binding
GO:0042802 identical protein binding
GO:0097718 disordered domain specific binding

Biological Process:
GO:0006308 DNA catabolic process
GO:0006309 apoptotic DNA fragmentation
GO:0006915 apoptotic process
GO:0030263 apoptotic chromosome condensation
GO:0051260 protein homooligomerization

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  BC048797 - Homo sapiens DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase), mRNA (cDNA clone MGC:51917 IMAGE:5204996), complete cds.
BC032827 - Homo sapiens DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase), mRNA (cDNA clone IMAGE:4820856), complete cds.
AB028911 - Homo sapiens DFF40 beta mRNA for DNA fragmentation factor 40 kDa subunit beta, complete cds.
AB028912 - Homo sapiens DFF40 gamma mRNA for DNA fragmentation factor 40 kDa subunit gamma, complete cds.
AB028913 - Homo sapiens DFF40 delta mRNA for DNA fragmentation factor 40 kDa subunit delta, complete cds.
AF064019 - Homo sapiens DNA fragmentation factor 40 kDa subunit (DFF40) mRNA, complete cds.
AK027141 - Homo sapiens cDNA: FLJ23488 fis, clone LNG00589, highly similar to AF064019 Homo sapiens DNA fragmentation factor 40 kDa subunit (DFF40) mRNA.
AK303065 - Homo sapiens cDNA FLJ50316 complete cds, highly similar to DNA fragmentation factor subunit beta (EC 3.-.-.-).
AK290877 - Homo sapiens cDNA FLJ76791 complete cds, highly similar to Homo sapiens DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase) (DFFB), transcript variant 1, mRNA.
JD477590 - Sequence 458614 from Patent EP1572962.
AK309316 - Homo sapiens cDNA, FLJ99357.
JD203623 - Sequence 184647 from Patent EP1572962.
JD056255 - Sequence 37279 from Patent EP1572962.
JD195113 - Sequence 176137 from Patent EP1572962.
JD136841 - Sequence 117865 from Patent EP1572962.
AF409060 - Homo sapiens DNA fragmentation factor B truncated form I (DFFB) mRNA, complete cds, alternatively spliced.
AF409061 - Homo sapiens DNA fragmentation factor B truncated form II (DFFB) mRNA, complete cds, alternatively spliced.
AF409062 - Homo sapiens DNA fragmentation factor B truncated form III (DFFB) mRNA, complete cds, alternatively spliced.
KJ896701 - Synthetic construct Homo sapiens clone ccsbBroadEn_06095 DFFB gene, encodes complete protein.
AB013918 - Homo sapiens mRNA for CAD, complete cds.
AF039210 - Homo sapiens caspase-activated nuclease mRNA, complete cds.
AY438267 - Homo sapiens c-truncated caspase-activated DNase mRNA, complete cds; aberrantly spliced.
AY438268 - Homo sapiens c-truncated caspase-activated DNase mRNA, complete cds; aberrantly spliced.
JD299069 - Sequence 280093 from Patent EP1572962.
JD280607 - Sequence 261631 from Patent EP1572962.
JD507789 - Sequence 488813 from Patent EP1572962.
JD364357 - Sequence 345381 from Patent EP1572962.
JD513924 - Sequence 494948 from Patent EP1572962.
JD513925 - Sequence 494949 from Patent EP1572962.
JD069743 - Sequence 50767 from Patent EP1572962.
JD414835 - Sequence 395859 from Patent EP1572962.
JD414840 - Sequence 395864 from Patent EP1572962.
JD251849 - Sequence 232873 from Patent EP1572962.
JD120572 - Sequence 101596 from Patent EP1572962.
JD379687 - Sequence 360711 from Patent EP1572962.
JD379688 - Sequence 360712 from Patent EP1572962.
JD379690 - Sequence 360714 from Patent EP1572962.
JD311821 - Sequence 292845 from Patent EP1572962.
JD311822 - Sequence 292846 from Patent EP1572962.
JD081619 - Sequence 62643 from Patent EP1572962.
JD081618 - Sequence 62642 from Patent EP1572962.
JD438367 - Sequence 419391 from Patent EP1572962.
JD223659 - Sequence 204683 from Patent EP1572962.
JD133766 - Sequence 114790 from Patent EP1572962.
JD240979 - Sequence 222003 from Patent EP1572962.
JD234567 - Sequence 215591 from Patent EP1572962.
JD545744 - Sequence 526768 from Patent EP1572962.
JD355717 - Sequence 336741 from Patent EP1572962.
JD355958 - Sequence 336982 from Patent EP1572962.
JD483266 - Sequence 464290 from Patent EP1572962.
JD240899 - Sequence 221923 from Patent EP1572962.
JD367253 - Sequence 348277 from Patent EP1572962.
JD325954 - Sequence 306978 from Patent EP1572962.
JD153342 - Sequence 134366 from Patent EP1572962.
JD527726 - Sequence 508750 from Patent EP1572962.
JD161705 - Sequence 142729 from Patent EP1572962.
JD523542 - Sequence 504566 from Patent EP1572962.
JD262073 - Sequence 243097 from Patent EP1572962.
JD165226 - Sequence 146250 from Patent EP1572962.
JD560950 - Sequence 541974 from Patent EP1572962.
JD542913 - Sequence 523937 from Patent EP1572962.
JD547760 - Sequence 528784 from Patent EP1572962.
JD213062 - Sequence 194086 from Patent EP1572962.
JD407504 - Sequence 388528 from Patent EP1572962.
JD095289 - Sequence 76313 from Patent EP1572962.
JD374566 - Sequence 355590 from Patent EP1572962.
JD489243 - Sequence 470267 from Patent EP1572962.
JD489244 - Sequence 470268 from Patent EP1572962.
JD072220 - Sequence 53244 from Patent EP1572962.
JD505144 - Sequence 486168 from Patent EP1572962.
JD099343 - Sequence 80367 from Patent EP1572962.
JD242577 - Sequence 223601 from Patent EP1572962.
JD242576 - Sequence 223600 from Patent EP1572962.
JD374853 - Sequence 355877 from Patent EP1572962.
JD157399 - Sequence 138423 from Patent EP1572962.
JD115949 - Sequence 96973 from Patent EP1572962.
JD106917 - Sequence 87941 from Patent EP1572962.
JD075193 - Sequence 56217 from Patent EP1572962.
JD377503 - Sequence 358527 from Patent EP1572962.
JD088199 - Sequence 69223 from Patent EP1572962.
JD532121 - Sequence 513145 from Patent EP1572962.
JD334502 - Sequence 315526 from Patent EP1572962.
JD428181 - Sequence 409205 from Patent EP1572962.
JD268667 - Sequence 249691 from Patent EP1572962.
JD513119 - Sequence 494143 from Patent EP1572962.
JD298698 - Sequence 279722 from Patent EP1572962.
JD352875 - Sequence 333899 from Patent EP1572962.
JD542205 - Sequence 523229 from Patent EP1572962.
JD424818 - Sequence 405842 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04210 - Apoptosis

BioCarta from NCI Cancer Genome Anatomy Project
h_setPathway - Granzyme A mediated Apoptosis Pathway
h_caspasePathway - Caspase Cascade in Apoptosis
h_mitochondriaPathway - Role of Mitochondria in Apoptotic Signaling
h_deathPathway - Induction of apoptosis through DR3 and DR4/5 Death Receptors
h_tnfr1Pathway - TNFR1 Signaling Pathway
h_fasPathway - FAS signaling pathway ( CD95 )
h_DNAfragmentPathway - Apoptotic DNA fragmentation and tissue homeostasis
h_HivnefPathway - HIV-I Nef: negative effector of Fas and TNF

Reactome (by CSHL, EBI, and GO)

Protein O76075 (Reactome details) participates in the following event(s):

R-HSA-211193 Homodimerization of DFF40
R-HSA-211207 Cleaved fragments of DFF45 dissociate from DFF40
R-HSA-211224 Association of DFF40 with DFF45
R-HSA-211186 Cleavage of DFF45 (224) by caspase-3
R-HSA-211190 Caspase 3-mediated cleavage of DFF45 (117)
R-HSA-211191 Association of DFF with alpha:beta importin
R-HSA-211206 Translocation of DFF to the nucleus
R-HSA-211239 Association of DFF40 with chromatin
R-HSA-211247 Cleavage of DNA by DFF40
R-HSA-211227 Activation of DNA fragmentation factor
R-HSA-140342 Apoptosis induced DNA fragmentation
R-HSA-75153 Apoptotic execution phase
R-HSA-109581 Apoptosis
R-HSA-5357801 Programmed Cell Death

-  Other Names for This Gene
  Alternate Gene Symbols: CAD, DFF2, DFF40, DFFB_HUMAN, NM_004402, NP_004393, O60521, O76075, Q5SR22, Q9BYI4, Q9BYI5, Q9BYI6
UCSC ID: uc001alc.3
RefSeq Accession: NM_004402
Protein: O76075 (aka DFFB_HUMAN)
CCDS: CCDS52.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004402.2
exon count: 7CDS single in 3' UTR: no RNA size: 3034
ORF size: 1017CDS single in intron: no Alignment % ID: 99.97
txCdsPredict score: 1881.00frame shift in genome: no % Coverage: 99.80
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.