Dffa (DNA fragmentation factor subunit alpha) - Rat Genome Database

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Gene: Dffa (DNA fragmentation factor subunit alpha) Rattus norvegicus
Analyze
Symbol: Dffa
Name: DNA fragmentation factor subunit alpha
RGD ID: 620334
Description: Predicted to have deoxyribonuclease inhibitor activity; protein domain specific binding activity; and protein folding chaperone. Predicted to be involved in several processes, including negative regulation of DNA metabolic process; regulation of apoptotic process; and thymocyte apoptotic process. Localizes to nucleus. Orthologous to human DFFA (DNA fragmentation factor subunit alpha); PARTICIPATES IN apoptotic cell death pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DNA fragmentation factor, alpha polypeptide; DNA fragmentation factor, alpha subunit; ICAD-S
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
mRatBN7.25159,540,718 - 159,553,639 (+)NCBI
Rnor_6.0 Ensembl5165,922,915 - 165,935,821 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.05165,922,893 - 165,935,822 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05169,573,089 - 169,586,003 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45166,179,130 - 166,192,029 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15166,189,332 - 166,200,048 (+)NCBI
Celera5157,811,683 - 157,824,582 (+)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
(+)-catechin  (ISO)
(+)-dexrazoxane  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dichloroethane  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
4-hydroxynon-2-enal  (ISO)
5-aza-2'-deoxycytidine  (ISO)
[6]-Shogaol  (ISO)
aclacinomycin A  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP,ISO)
atrazine  (ISO)
benzene  (EXP)
benzo[a]pyrene  (EXP,ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
capsaicin  (ISO)
carbamazepine  (ISO)
celecoxib  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (ISO)
daunorubicin  (ISO)
decabromodiphenyl ether  (EXP)
deoxynivalenol  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (EXP,ISO)
diclofenac  (ISO)
dimethyl sulfoxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ellagic acid  (ISO)
embelin  (ISO)
enzyme inhibitor  (ISO)
equol  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
folic acid  (ISO)
furosemide  (EXP)
genistein  (ISO)
glyphosate  (ISO)
hydrogen peroxide  (EXP)
isoflurane  (EXP)
metformin  (ISO)
methyl methanesulfonate  (ISO)
Mitotane  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nickel atom  (ISO)
ochratoxin A  (EXP)
oxybenzone  (EXP)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
Parthenin  (ISO)
pentobarbital  (EXP)
phenylmercury acetate  (ISO)
piroxicam  (ISO)
pterostilbene  (ISO)
quercetin  (EXP,ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sunitinib  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9108473   PMID:9564035   PMID:10601318   PMID:11371636   PMID:12477932   PMID:14663139   PMID:15572351   PMID:19882353   PMID:19944011   PMID:22253444  


Genomics

Comparative Map Data
Dffa
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25159,540,718 - 159,553,639 (+)NCBI
Rnor_6.0 Ensembl5165,922,915 - 165,935,821 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.05165,922,893 - 165,935,822 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05169,573,089 - 169,586,003 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45166,179,130 - 166,192,029 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15166,189,332 - 166,200,048 (+)NCBI
Celera5157,811,683 - 157,824,582 (+)NCBICelera
Cytogenetic Map5q36NCBI
DFFA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl110,456,522 - 10,472,529 (-)EnsemblGRCh38hg38GRCh38
GRCh38110,456,522 - 10,472,529 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37110,516,579 - 10,532,586 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36110,443,175 - 10,455,200 (-)NCBINCBI36hg18NCBI36
Celera19,631,993 - 9,644,017 (-)NCBI
Cytogenetic Map1p36.22NCBI
HuRef19,674,182 - 9,686,174 (-)NCBIHuRef
CHM1_1110,508,330 - 10,520,370 (-)NCBICHM1_1
Dffa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394149,188,599 - 149,205,110 (+)NCBIGRCm39mm39
GRCm39 Ensembl4149,188,603 - 149,205,104 (+)Ensembl
GRCm384149,104,142 - 149,120,653 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4149,104,146 - 149,120,647 (+)EnsemblGRCm38mm10GRCm38
MGSCv374148,478,262 - 148,494,759 (+)NCBIGRCm37mm9NCBIm37
MGSCv364147,947,953 - 147,964,450 (+)NCBImm8
Celera4151,371,738 - 151,386,868 (+)NCBICelera
Cytogenetic Map4E2NCBI
Dffa
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554863,273,712 - 3,274,510 (+)NCBIChiLan1.0ChiLan1.0
DFFA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1110,445,553 - 10,457,547 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl110,445,553 - 10,457,547 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v019,221,096 - 9,232,813 (-)NCBIMhudiblu_PPA_v0panPan3
DFFA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1285,364,819 - 85,372,473 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl285,364,851 - 85,373,772 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha281,966,306 - 81,973,968 (+)NCBI
ROS_Cfam_1.0286,099,825 - 86,107,488 (+)NCBI
UMICH_Zoey_3.1282,847,197 - 82,854,858 (+)NCBI
UNSW_CanFamBas_1.0283,849,698 - 83,857,360 (+)NCBI
UU_Cfam_GSD_1.0284,912,608 - 84,920,270 (+)NCBI
Dffa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505833,811,757 - 33,821,826 (-)NCBI
SpeTri2.0NW_0049366234,296,995 - 4,307,069 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DFFA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl670,724,587 - 70,736,236 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1670,725,403 - 70,736,264 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2664,658,250 - 64,669,091 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DFFA
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120121,312,291 - 121,324,055 (+)NCBI
ChlSab1.1 Ensembl20121,311,954 - 121,323,402 (+)Ensembl
Dffa
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248182,225,777 - 2,239,897 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5149568588167739697Rat
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
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5149029982173687766Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5157212422167739539Rat
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
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
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5128687766173687766Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133943857173707219Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133943857173707219Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5134197905173707219Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)547745646167946134Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5157319671171194163Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5161084664173707219Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5150360936167946134Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
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
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5134712342173707219Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5131077716173707219Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:568
Count of miRNA genes:265
Interacting mature miRNAs:357
Transcripts:ENSRNOT00000059522
Prediction methods:Microtar, 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 36 17 12 9 12 8 11 66 28 32 11 8
Low 7 40 29 10 29 8 7 9
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000059522   ⟹   ENSRNOP00000063043
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5165,922,923 - 165,935,821 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089179   ⟹   ENSRNOP00000070485
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5165,922,915 - 165,935,820 (+)Ensembl
RefSeq Acc Id: NM_053679   ⟹   NP_446131
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25159,540,738 - 159,553,639 (+)NCBI
Rnor_6.05165,922,923 - 165,935,822 (+)NCBI
Rnor_5.05169,573,089 - 169,586,003 (+)NCBI
RGSC_v3.45166,179,130 - 166,192,029 (+)RGD
Celera5157,811,683 - 157,824,582 (+)RGD
Sequence:
RefSeq Acc Id: XM_006239362   ⟹   XP_006239424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25159,540,718 - 159,553,636 (+)NCBI
Rnor_6.05165,922,893 - 165,935,819 (+)NCBI
Rnor_5.05169,573,089 - 169,586,003 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_446131 (Get FASTA)   NCBI Sequence Viewer  
  XP_006239424 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF61425 (Get FASTA)   NCBI Sequence Viewer  
  AAI00068 (Get FASTA)   NCBI Sequence Viewer  
  EDL81148 (Get FASTA)   NCBI Sequence Viewer  
  EDL81149 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446131   ⟸   NM_053679
- UniProtKB: Q498U6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239424   ⟸   XM_006239362
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JY18 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070485   ⟸   ENSRNOT00000089179
RefSeq Acc Id: ENSRNOP00000063043   ⟸   ENSRNOT00000059522
Protein Domains
CIDE-N

Transcriptome

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

Promoters
RGD ID:13694268
Promoter ID:EPDNEW_R4793
Type:multiple initiation site
Name:Dffa_1
Description:DNA fragmentation factor subunit alpha
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05165,922,966 - 165,923,026EPDNEW

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)
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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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
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
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 165932976 165932977 T G snv F344/NRrrc (MCW)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 166189183 166189184 T G snv F344/NRrrc (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620334 AgrOrtholog
Ensembl Genes ENSRNOG00000013603 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063043 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070485 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000059522 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000089179 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7389030 IMAGE-MGC_LOAD
InterPro CAD UniProtKB/TrEMBL
  DFF-C_dom UniProtKB/TrEMBL
  DNA_fragmentation_C UniProtKB/TrEMBL
  DNA_fragmentation_factor_asu UniProtKB/TrEMBL
KEGG Report rno:114214 UniProtKB/TrEMBL
MGC_CLONE MGC:112608 IMAGE-MGC_LOAD
NCBI Gene 114214 ENTREZGENE
PANTHER PTHR12306:SF16 UniProtKB/TrEMBL
Pfam CIDE-N UniProtKB/TrEMBL
  DFF-C UniProtKB/TrEMBL
PhenoGen Dffa PhenoGen
PIRSF DFF_alpha UniProtKB/TrEMBL
PROSITE CIDE_N UniProtKB/TrEMBL
SMART CAD UniProtKB/TrEMBL
Superfamily-SCOP SSF81783 UniProtKB/TrEMBL
UniProt A0A0G2JY18 ENTREZGENE, UniProtKB/TrEMBL
  Q498U6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-26 Dffa  DNA fragmentation factor subunit alpha  Dffa  DNA fragmentation factor, alpha polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-02-25 Dffa  DNA fragmentation factor, alpha polypeptide  Dffa  DNA fragmentation factor, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Dffa  DNA fragmentation factor, alpha subunit      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Dffa  DNA fragmentation factor, alpha subunit      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to the nucleus 632505
gene_physical_interaction forms a complex with DFF40/caspase-activated DNase (CAD) 632505