Dffb (DNA fragmentation factor subunit beta) - Rat Genome Database
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Gene: Dffb (DNA fragmentation factor subunit beta) Rattus norvegicus
Analyze
Symbol: Dffb
Name: DNA fragmentation factor subunit beta
RGD ID: 620335
Description: Exhibits deoxyribonuclease activity. Involved in apoptotic DNA fragmentation and brain development. Localizes to nucleus. Biomarker of transient cerebral ischemia. Orthologous to human DFFB (DNA fragmentation factor subunit beta); PARTICIPATES IN apoptotic cell death pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cad; caspase-activated deoxyribonuclease; caspase-activated DNase; DFF-40; DNA fragmentation factor 40 kD beta polypeptide (caspase-activated DNase); 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
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.05171,250,559 - 171,261,875 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5171,249,633 - 171,262,119 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05174,742,181 - 174,753,497 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45170,750,718 - 170,762,034 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15170,761,212 - 170,772,529 (-)NCBI
Celera5162,735,202 - 162,746,518 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dimethylhydrazine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-methylcholine  (ISO)
2-naphthylamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-hydroxynon-2-enal  (ISO)
5-aza-2'-deoxycytidine  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
calcitriol  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dichloroacetic acid  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
disodium selenite  (ISO)
doxorubicin  (ISO)
fenvalerate  (EXP)
flavonoids  (EXP)
genistein  (ISO)
hydroquinone  (ISO)
indometacin  (ISO)
irinotecan  (ISO)
isoprenaline  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
methotrexate  (ISO)
Mitotane  (EXP)
motexafin gadolinium  (ISO)
N-acetylsphingosine  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-ethyl-N-nitrosourea  (ISO)
nicotine  (ISO)
nitric oxide  (EXP)
ochratoxin A  (EXP)
p-menthan-3-ol  (ISO)
paracetamol  (ISO)
pirinixic acid  (ISO)
quercetin  (ISO)
reactive oxygen species  (ISO)
Roridin A  (ISO)
rotenone  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
sulindac  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP)
tributylstannane  (ISO)
valproic acid  (ISO)
vincaleukoblastine  (ISO)
zinc acetate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromatin  (ISO)
cytoplasm  (IEA)
cytosol  (ISO)
nucleolus  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IDA,ISO)
protein-containing complex  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9108473   PMID:10959840   PMID:11371636   PMID:12477932   PMID:15167901   PMID:15572351   PMID:15644269   PMID:16767516   PMID:19882353   PMID:19944011   PMID:22253444  


Genomics

Comparative Map Data
Dffb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.05171,250,559 - 171,261,875 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5171,249,633 - 171,262,119 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05174,742,181 - 174,753,497 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45170,750,718 - 170,762,034 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15170,761,212 - 170,772,529 (-)NCBI
Celera5162,735,202 - 162,746,518 (-)NCBICelera
Cytogenetic Map5q36NCBI
DFFB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl13,857,267 - 3,885,429 (+)EnsemblGRCh38hg38GRCh38
GRCh3813,857,286 - 3,885,429 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3713,773,845 - 3,801,993 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3613,763,705 - 3,791,853 (+)NCBINCBI36hg18NCBI36
Build 3413,797,001 - 3,825,149NCBI
Celera13,028,085 - 3,056,136 (+)NCBI
Cytogenetic Map1p36.32NCBI
HuRef13,069,403 - 3,097,689 (+)NCBIHuRef
CHM1_113,760,834 - 3,789,006 (+)NCBICHM1_1
Dffb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394154,048,904 - 154,059,578 (-)NCBIGRCm39mm39
GRCm384153,964,447 - 153,975,121 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4153,964,449 - 153,975,126 (-)EnsemblGRCm38mm10GRCm38
MGSCv374153,338,558 - 153,349,190 (-)NCBIGRCm37mm9NCBIm37
MGSCv364152,808,255 - 152,818,926 (-)NCBImm8
Celera4156,252,603 - 156,263,261 (-)NCBICelera
Cytogenetic Map4E2NCBI
Dffb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554867,838,273 - 7,850,180 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554867,836,013 - 7,849,875 (-)NCBIChiLan1.0ChiLan1.0
DFFB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113,649,723 - 3,676,896 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13,649,729 - 3,676,896 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012,529,733 - 2,559,490 (+)NCBIMhudiblu_PPA_v0panPan3
DFFB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl558,339,634 - 58,354,326 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1558,340,183 - 58,355,353 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dffb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493673779,789 - 96,140 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DFFB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl665,310,863 - 65,323,816 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1665,310,868 - 65,323,816 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2660,157,486 - 60,164,636 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DFFB
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120127,800,351 - 127,823,512 (-)NCBI
Dffb
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248186,700,120 - 6,712,449 (-)NCBI

Position Markers
BE121446  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05171,250,375 - 171,250,537NCBIRnor6.0
Rnor_5.05174,741,997 - 174,742,159UniSTSRnor5.0
RGSC_v3.45170,750,534 - 170,750,696UniSTSRGSC3.4
Celera5162,735,018 - 162,735,180UniSTS
Cytogenetic Map5q36UniSTS
RH 3.4 Map51142.0UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5142307322173707219Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5136354114173707219Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136640731173707219Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5134712342173707219Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5157319671173707219Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138154677172402610Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5134197905173707219Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5134712342173707219Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5149029982173687766Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5131077716173707219Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5161084664173707219Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133943857173707219Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5142309061173707219Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132551937173707219Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133943857173707219Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5128687766173687766Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:146
Count of miRNA genes:102
Interacting mature miRNAs:121
Transcripts:ENSRNOT00000032825
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 4 2 2 2 2 32 20 27 1
Low 39 55 39 17 39 8 11 42 15 14 10 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000032825   ⟹   ENSRNOP00000034722
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5171,249,633 - 171,262,119 (-)Ensembl
RefSeq Acc Id: NM_053362   ⟹   NP_445814
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05171,250,559 - 171,261,875 (-)NCBI
Rnor_5.05174,742,181 - 174,753,497 (-)NCBI
RGSC_v3.45170,750,718 - 170,762,034 (-)RGD
Celera5162,735,202 - 162,746,518 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_445814 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK16646 (Get FASTA)   NCBI Sequence Viewer  
  EDL81250 (Get FASTA)   NCBI Sequence Viewer  
  Q99N34 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_445814   ⟸   NM_053362
- UniProtKB: Q99N34 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000034722   ⟸   ENSRNOT00000032825
Protein Domains
CIDE-N

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620335 AgrOrtholog
Ensembl Genes ENSRNOG00000025030 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000034722 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000032825 ENTREZGENE, UniProtKB/TrEMBL
InterPro CIDE-N_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DFF40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DFF40_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84359 UniProtKB/Swiss-Prot
NCBI Gene 84359 ENTREZGENE
PANTHER PTHR13067 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CIDE-N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DFF40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Dffb PhenoGen
PROSITE CIDE_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CAD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.67077 ENTREZGENE
UniProt A0A0H2UHU4_RAT UniProtKB/TrEMBL
  DFFB_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Dffb  DNA fragmentation factor subunit beta  Dffb  DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-10 Dffb  DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase)  Dffb  DNA fragmentation factor, beta polypeptide (caspase-activated DNase)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-26 Dffb  DNA fragmentation factor, beta polypeptide (caspase-activated DNase)  Dffb  DNA fragmentation factor, beta subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Dffb  DNA fragmentation factor, beta subunit    DNA fragmentation factor, 40 kD, beta polypeptide (caspase-activated DNase)  Name updated 1299863 APPROVED
2002-08-07 Dffb  DNA fragmentation factor, 40 kD, beta polypeptide (caspase-activated DNase)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains a probable nuclear localization segment stretch of 20 amino acid stretch and a N terminal cysteine residue stretch acting as heterodimerization component 628524
gene_expression highest mRNA expression in intestine and medium expression in the spleen, lung, kidney, liver, testis, heart and brain; low expression in stomach an skeletal muscle 628524
gene_expression ~4.5 fold higher cerebellar expression in 17-d-old embryos and 1- and 2-week-old newborns than adults 628524
gene_function caspase-3 activated endogenous deoxyribonuclease 628524
gene_homology has 73% and 94% identity to human and mouse genes, respectively 628524
gene_pathway active in neuronal apoptotic pathway 628524
gene_physical_interaction forms a heterodimeric complex with caspase-activated deoxyribonuclease (CAD) in the nucleus 628524
gene_process promotes apoptotic internucleosomal DNA degradation 628524
gene_process promotes DNA degradations related nuclear alterations in ischemic neurons 628524
gene_regulation DNA degradation inhibited by ICAD prtein levels 628524
gene_regulation activated by caspase-3 and induced after ischemia 628524