Tdp1 (tyrosyl-DNA phosphodiesterase 1) - Rat Genome Database
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Gene: Tdp1 (tyrosyl-DNA phosphodiesterase 1) Rattus norvegicus
Analyze
Symbol: Tdp1
Name: tyrosyl-DNA phosphodiesterase 1
RGD ID: 1309618
Description: Predicted to have 3'-tyrosyl-DNA phosphodiesterase activity; double-stranded DNA binding activity; and single-stranded DNA binding activity. Predicted to be involved in double-strand break repair and single strand break repair. Predicted to localize to cytoplasm; nucleoplasm; and plasma membrane. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 1 with axonal neuropathy. Orthologous to human TDP1 (tyrosyl-DNA phosphodiesterase 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC314380; MGC112732; tyr-DNA phosphodiesterase 1
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_6.06123,895,860 - 123,963,688 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6123,897,956 - 123,963,675 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06133,109,211 - 133,187,083 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46124,095,259 - 124,162,815 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16124,105,017 - 124,166,344 (+)NCBI
Celera6116,696,845 - 116,764,588 (+)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12023295   PMID:12477932   PMID:15811850   PMID:17118488   PMID:17576665   PMID:17600775   PMID:17914460   PMID:17948061   PMID:21390131   PMID:22822062  


Genomics

Comparative Map Data
Tdp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.06123,895,860 - 123,963,688 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6123,897,956 - 123,963,675 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06133,109,211 - 133,187,083 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46124,095,259 - 124,162,815 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16124,105,017 - 124,166,344 (+)NCBI
Celera6116,696,845 - 116,764,588 (+)NCBICelera
Cytogenetic Map6q32NCBI
TDP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1489,954,939 - 90,044,764 (+)EnsemblGRCh38hg38GRCh38
GRCh381489,954,923 - 90,044,768 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371490,421,944 - 90,511,108 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361489,491,999 - 89,580,861 (+)NCBINCBI36hg18NCBI36
Build 341489,491,998 - 89,580,859NCBI
Celera1470,469,447 - 70,558,298 (+)NCBI
Cytogenetic Map14q32.11NCBI
HuRef1470,596,174 - 70,685,067 (+)NCBIHuRef
CHM1_11490,360,149 - 90,448,932 (+)NCBICHM1_1
Tdp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391299,850,767 - 99,921,482 (+)NCBIGRCm39mm39
GRCm381299,884,515 - 99,955,223 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1299,884,517 - 99,955,219 (+)EnsemblGRCm38mm10GRCm38
MGSCv3712101,122,725 - 101,193,429 (+)NCBIGRCm37mm9NCBIm37
MGSCv3612100,285,568 - 100,338,412 (+)NCBImm8
Celera12101,107,017 - 101,181,494 (+)NCBICelera
Cytogenetic Map12ENCBI
Tdp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543812,421,005 - 12,511,493 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543812,421,790 - 12,510,243 (+)NCBIChiLan1.0ChiLan1.0
TDP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11489,926,462 - 90,014,802 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1489,926,462 - 90,014,802 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01470,574,066 - 70,662,562 (+)NCBIMhudiblu_PPA_v0panPan3
TDP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl861,024,084 - 61,107,506 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1861,023,564 - 61,107,599 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tdp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493648817,237,002 - 17,311,325 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TDP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl7111,767,089 - 111,853,257 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17111,767,094 - 111,853,262 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27118,331,680 - 118,417,900 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TDP1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12467,672,178 - 67,762,340 (+)NCBI
Tdp1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473412,319,499 - 12,414,815 (-)NCBI

Position Markers
RH129987  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06123,963,418 - 123,963,604NCBIRnor6.0
Rnor_5.06133,186,817 - 133,187,003UniSTSRnor5.0
RGSC_v3.46124,162,549 - 124,162,735UniSTSRGSC3.4
Celera6116,764,322 - 116,764,508UniSTS
Cytogenetic Map6q32UniSTS
RH 3.4 Map6871.2UniSTS
RH142247  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06123,963,413 - 123,963,592NCBIRnor6.0
Rnor_5.06133,186,812 - 133,186,991UniSTSRnor5.0
RGSC_v3.46124,162,544 - 124,162,723UniSTSRGSC3.4
Celera6116,764,317 - 116,764,496UniSTS
Cytogenetic Map6q32UniSTS
RH 3.4 Map6871.2UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)688507712133507712Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)689631358134631358Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)689631358134631358Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)697949772133849286Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6104363890147991367Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6104381930138066274Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6108154445133849286Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6111134524138065254Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6117355600147991367Rat
1298087Iddm18Insulin dependent diabetes mellitus QTL 180.0001urine glucose amount (VT:0001758)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)6121224054135658578Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:165
Count of miRNA genes:126
Interacting mature miRNAs:138
Transcripts:ENSRNOT00000005167
Prediction methods:Microtar, Miranda, Rnahybrid
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 1 2 17 12 6 12 43 18 34
Low 2 41 40 29 13 29 8 11 31 17 7 11 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005167   ⟹   ENSRNOP00000005167
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6123,897,956 - 123,963,675 (+)Ensembl
RefSeq Acc Id: NM_001031657   ⟹   NP_001026827
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06123,895,860 - 123,963,684 (+)NCBI
Rnor_5.06133,109,211 - 133,187,083 (+)NCBI
RGSC_v3.46124,095,259 - 124,162,815 (+)RGD
Celera6116,696,845 - 116,764,588 (+)RGD
Sequence:
RefSeq Acc Id: XM_006240432   ⟹   XP_006240494
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06123,898,131 - 123,963,688 (+)NCBI
Rnor_5.06133,109,211 - 133,187,083 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001026827 (Get FASTA)   NCBI Sequence Viewer  
  XP_006240494 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH98739 (Get FASTA)   NCBI Sequence Viewer  
  EDL81708 (Get FASTA)   NCBI Sequence Viewer  
  EDL81709 (Get FASTA)   NCBI Sequence Viewer  
  Q4G056 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001026827   ⟸   NM_001031657
- UniProtKB: Q4G056 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006240494   ⟸   XM_006240432
- Peptide Label: isoform X1
- UniProtKB: A0A0H2UHC3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000005167   ⟸   ENSRNOT00000005167

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)
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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: 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
6 123902088 123902089 G C snv MR/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 124101487 124101488 G C snv MR/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309618 AgrOrtholog
Ensembl Genes ENSRNOG00000003831 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005167 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005167 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.870.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7385935 IMAGE-MGC_LOAD
InterPro Tdp1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TDP_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:314380 UniProtKB/Swiss-Prot
MGC_CLONE MGC:112732 IMAGE-MGC_LOAD
NCBI Gene 314380 ENTREZGENE
PANTHER PTHR12415 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Tyr-DNA_phospho UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB TDP1 RGD
PhenoGen Tdp1 PhenoGen
UniGene Rn.12661 ENTREZGENE
UniProt A0A0H2UHC3 ENTREZGENE, UniProtKB/TrEMBL
  Q4G056 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Tdp1  tyrosyl-DNA phosphodiesterase 1  Tdp1_predicted  tyrosyl-DNA phosphodiesterase 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tdp1_predicted  tyrosyl-DNA phosphodiesterase 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED