Tfdp1 (transcription factor Dp-1) - Rat Genome Database

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Gene: Tfdp1 (transcription factor Dp-1) Rattus norvegicus
Analyze
Symbol: Tfdp1
Name: transcription factor Dp-1
RGD ID: 1560344
Description: Is predicted to contribute to DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including anoikis; positive regulation of G1/S transition of mitotic cell cycle; and regulation of cellular macromolecule biosynthetic process. Predicted to localize to RNA polymerase II transcription regulator complex; cytosol; and nucleoplasm. Orthologous to several human genes including TFDP1 (transcription factor Dp-1); PARTICIPATES IN cell cycle pathway, mitotic; transforming growth factor-beta superfamily mediated signaling pathway; INTERACTS WITH bisphenol A; finasteride; flutamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: hypothetical protein LOC361178; MGC112830; similar to transcription factor; uncharacterized protein LOC361178
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
mRatBN7.21676,162,040 - 76,200,871 (-)NCBI
Rnor_6.0 Ensembl1681,089,292 - 81,127,257 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01681,088,642 - 81,127,244 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01680,578,421 - 80,615,804 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41681,018,040 - 81,056,049 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1673,969,240 - 74,007,155 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
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)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-methylcholine  (ISO)
2-naphthylamine  (ISO)
3-[3-(tert-butylsulfanyl)-1-(4-chlorobenzyl)-5-(propan-2-yl)-1H-indol-2-yl]-2,2-dimethylpropanoic acid  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
5-fluorouracil  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
cerium trichloride  (ISO)
chlorpromazine  (ISO)
chromium(6+)  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
diarsenic trioxide  (ISO)
diclofenac  (ISO)
disodium selenite  (ISO)
Enterolactone  (ISO)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
genistein  (EXP)
geraniol  (ISO)
glyphosate  (ISO)
GW 3965  (ISO)
hydralazine  (ISO)
methapyrilene  (EXP,ISO)
methyl methanesulfonate  (ISO)
methylparaben  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (ISO)
nicotine  (ISO)
p-menthan-3-ol  (ISO)
paracetamol  (ISO)
perfluorooctanoic acid  (ISO)
phenylephrine  (EXP)
phytoestrogen  (ISO)
pirinixic acid  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
silver(1+) nitrate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
sulindac  (EXP)
tamibarotene  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (ISO)
toluene 2,4-diisocyanate  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
trovafloxacin  (EXP)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:7739537   PMID:7797074   PMID:10082561   PMID:11331592   PMID:14667810   PMID:15448153   PMID:16360038   PMID:17062573   PMID:20176812   PMID:25940086   PMID:27825926  


Genomics

Comparative Map Data
Tfdp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21676,162,040 - 76,200,871 (-)NCBI
Rnor_6.0 Ensembl1681,089,292 - 81,127,257 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01681,088,642 - 81,127,244 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01680,578,421 - 80,615,804 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41681,018,040 - 81,056,049 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1673,969,240 - 74,007,155 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
TFDP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl13113,584,721 - 113,641,473 (+)EnsemblGRCh38hg38GRCh38
GRCh3813113,584,688 - 113,641,473 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3713114,239,003 - 114,295,788 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3613113,287,057 - 113,343,505 (+)NCBINCBI36hg18NCBI36
Build 3413113,287,056 - 113,343,503NCBI
Celera1395,066,242 - 95,123,044 (+)NCBI
Cytogenetic Map13q34NCBI
HuRef1394,679,228 - 94,735,067 (+)NCBIHuRef
CHM1_113114,208,391 - 114,265,115 (+)NCBICHM1_1
Tfdp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39813,388,273 - 13,428,448 (+)NCBIGRCm39mm39
GRCm39 Ensembl813,388,751 - 13,428,448 (+)Ensembl
GRCm38813,338,725 - 13,378,448 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl813,338,751 - 13,378,448 (+)EnsemblGRCm38mm10GRCm38
MGSCv37813,339,674 - 13,377,702 (+)NCBIGRCm37mm9NCBIm37
MGSCv36813,339,651 - 13,377,679 (+)NCBImm8
Celera813,508,488 - 13,546,106 (+)NCBICelera
Cytogenetic Map8A1.1NCBI
Tfdp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955404368,793 - 408,930 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955404371,905 - 408,441 (-)NCBIChiLan1.0ChiLan1.0
TFDP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113113,789,280 - 113,840,831 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13113,789,280 - 113,840,825 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01394,730,343 - 94,789,328 (+)NCBIMhudiblu_PPA_v0panPan3
TFDP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12260,863,541 - 60,897,491 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2260,870,413 - 60,896,629 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2260,581,230 - 60,608,364 (+)NCBI
ROS_Cfam_1.02261,554,725 - 61,581,881 (+)NCBI
UMICH_Zoey_3.12260,993,491 - 61,020,624 (+)NCBI
UNSW_CanFamBas_1.02260,995,475 - 61,022,666 (+)NCBI
UU_Cfam_GSD_1.02261,026,641 - 61,053,745 (+)NCBI
Tfdp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945195,737,525 - 195,767,348 (+)NCBI
SpeTri2.0NW_004936472184,808 - 214,628 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TFDP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1178,755,345 - 78,778,310 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11178,755,472 - 78,778,312 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21186,489,486 - 86,511,644 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TFDP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1391,552,083 - 91,608,978 (+)NCBI
ChlSab1.1 Ensembl391,581,401 - 91,607,864 (+)Ensembl
Vero_WHO_p1.0NW_02366604648,635,469 - 48,695,876 (+)NCBI
Tfdp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624793481,791 - 515,142 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163900002184000021Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164151271086512710Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164151271086512710Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164655818890668790Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165781635790668790Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165781635790668790Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165781635790668790Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165928577589248943Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:512
Count of miRNA genes:238
Interacting mature miRNAs:281
Transcripts:ENSRNOT00000026150, ENSRNOT00000034274
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 3 43 56 40 19 40 8 11 74 35 41 11 8
Low 1 1 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001025718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253451 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771398 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771400 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094676 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094677 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094681 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094682 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC111257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC098789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC099767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000026150   ⟹   ENSRNOP00000026150
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1681,089,308 - 81,127,238 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087192   ⟹   ENSRNOP00000070337
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1681,089,292 - 81,127,257 (+)Ensembl
RefSeq Acc Id: NM_001025718   ⟹   NP_001020889
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,162,040 - 76,199,974 (-)NCBI
Rnor_6.01681,089,308 - 81,127,244 (+)NCBI
Rnor_5.01680,578,421 - 80,615,804 (+)NCBI
RGSC_v3.41681,018,040 - 81,056,049 (-)RGD
Celera1673,969,240 - 74,007,155 (-)RGD
Sequence:
RefSeq Acc Id: XM_006253451   ⟹   XP_006253513
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01681,089,110 - 81,127,241 (+)NCBI
Rnor_5.01680,578,421 - 80,615,804 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771397   ⟹   XP_008769619
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,162,040 - 76,200,676 (-)NCBI
Rnor_6.01681,088,642 - 81,127,241 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771398   ⟹   XP_008769620
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,162,040 - 76,200,438 (-)NCBI
Rnor_6.01681,088,844 - 81,127,241 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771400   ⟹   XP_008769622
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,162,040 - 76,200,438 (-)NCBI
Rnor_6.01681,089,110 - 81,127,241 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039094676   ⟹   XP_038950604
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,162,040 - 76,200,836 (-)NCBI
RefSeq Acc Id: XM_039094677   ⟹   XP_038950605
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,162,040 - 76,200,871 (-)NCBI
RefSeq Acc Id: XM_039094678   ⟹   XP_038950606
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,162,040 - 76,183,816 (-)NCBI
RefSeq Acc Id: XM_039094679   ⟹   XP_038950607
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,162,040 - 76,200,840 (-)NCBI
RefSeq Acc Id: XM_039094680   ⟹   XP_038950608
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,162,043 - 76,200,698 (-)NCBI
RefSeq Acc Id: XM_039094681   ⟹   XP_038950609
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,162,040 - 76,200,778 (-)NCBI
RefSeq Acc Id: XM_039094682   ⟹   XP_038950610
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,162,040 - 76,200,839 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001020889   ⟸   NM_001025718
- UniProtKB: Q4KM53 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253513   ⟸   XM_006253451
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008769619   ⟸   XM_008771397
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JXN0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769620   ⟸   XM_008771398
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JXN0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769622   ⟸   XM_008771400
- Peptide Label: isoform X3
- UniProtKB: G3V8H9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070337   ⟸   ENSRNOT00000087192
RefSeq Acc Id: ENSRNOP00000026150   ⟸   ENSRNOT00000026150
RefSeq Acc Id: XP_038950605   ⟸   XM_039094677
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038950607   ⟸   XM_039094679
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038950610   ⟸   XM_039094682
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038950604   ⟸   XM_039094676
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038950609   ⟸   XM_039094681
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038950606   ⟸   XM_039094678
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038950608   ⟸   XM_039094680
- Peptide Label: isoform X3
Protein Domains
DP   E2F_TDP

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)
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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
F344/NRrrc (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560344 AgrOrtholog
Ensembl Genes ENSRNOG00000019222 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000026150 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070337 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026150 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000087192 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
  1.20.140.80 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7375514 IMAGE-MGC_LOAD
InterPro DP-1 UniProtKB/TrEMBL
  E2F-DP_heterodim UniProtKB/TrEMBL
  E2F_TDP UniProtKB/TrEMBL
  TF_DP_C_sf UniProtKB/TrEMBL
  Transc_factor_DP_C UniProtKB/TrEMBL
  Transcrpt_fac_DP UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:361178 UniProtKB/TrEMBL
MGC_CLONE MGC:112830 IMAGE-MGC_LOAD
NCBI Gene 361178 ENTREZGENE
PANTHER PTHR12548 UniProtKB/TrEMBL
  PTHR12548:SF4 UniProtKB/TrEMBL
Pfam E2F_TDP UniProtKB/TrEMBL
  PF08781 UniProtKB/TrEMBL
PhenoGen Tfdp1 PhenoGen
PIRSF Transcription_factor_DP UniProtKB/TrEMBL
SMART E2F_TDP UniProtKB/TrEMBL
  SM01138 UniProtKB/TrEMBL
Superfamily-SCOP SSF144074 UniProtKB/TrEMBL
  SSF46785 UniProtKB/TrEMBL
UniProt A0A0G2JXN0 ENTREZGENE, UniProtKB/TrEMBL
  G3V8H9 ENTREZGENE, UniProtKB/TrEMBL
  Q4KM53 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-08-15 Tfdp1  transcription factor Dp-1  MGC112830  similar to transcription factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 MGC112830  similar to transcription factor      Symbol and Name status set to provisional 70820 PROVISIONAL