Tardbp (TAR DNA binding protein) - Rat Genome Database
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Gene: Tardbp (TAR DNA binding protein) Rattus norvegicus
Analyze
Symbol: Tardbp
Name: TAR DNA binding protein
RGD ID: 1310906
Description: Exhibits RNA binding activity. Involved in positive regulation of insulin secretion and response to endoplasmic reticulum stress. Localizes to cytoplasm and nuclear lumen. Human ortholog(s) of this gene implicated in Parkinson's disease; amyotrophic lateral sclerosis; amyotrophic lateral sclerosis type 10; and motor neuron disease. Orthologous to human TARDBP (TAR DNA binding protein); INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; bis(2-ethylhexyl) phthalate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC298648; TAR DNA-binding protein 43; Tdp-43
Orthologs:
Homo sapiens (human) : TARDBP (TAR DNA binding protein)  HGNC  Alliance
Mus musculus (house mouse) : Tardbp (TAR DNA binding protein)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Tardbp (TAR DNA binding protein)
Pan paniscus (bonobo/pygmy chimpanzee) : TARDBP (TAR DNA binding protein)
Canis lupus familiaris (dog) : TARDBP (TAR DNA binding protein)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Tardbp (TAR DNA binding protein)
Sus scrofa (pig) : TARDBP (TAR DNA binding protein)
Chlorocebus sabaeus (African green monkey) : TARDBP (TAR DNA binding protein)
Heterocephalus glaber (naked mole-rat) : Tardbp (TAR DNA binding protein)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.05165,432,089 - 165,442,232 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5165,432,095 - 165,442,048 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05169,088,684 - 169,099,216 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45165,698,665 - 165,709,531 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15165,708,851 - 165,719,708 (-)NCBI
Celera5157,327,910 - 157,337,955 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
5-aza-2'-deoxycytidine  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antimony(0)  (ISO)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bufalin  (ISO)
butanal  (ISO)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
carbonyl cyanide p-trifluoromethoxyphenylhydrazone  (ISO)
chloroprene  (ISO)
chloroquine  (ISO)
chromium(6+)  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxycycline  (ISO)
emetine  (ISO)
entinostat  (ISO)
enzyme inhibitor  (ISO)
epoxomicin  (ISO)
fenvalerate  (EXP)
flutamide  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
glafenine  (EXP)
hydroquinone  (ISO)
hydroquinone O-beta-D-glucopyranoside  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
mercury atom  (ISO)
mercury dichloride  (EXP)
mercury(0)  (ISO)
methylmercury chloride  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosomorpholine  (EXP)
nefazodone  (EXP)
nickel dichloride  (ISO)
nimesulide  (EXP)
Nonylphenol  (EXP)
ochratoxin A  (ISO)
oxaliplatin  (EXP)
paraquat  (ISO)
pentanal  (ISO)
PF-670462  (ISO)
phenobarbital  (ISO)
phenol  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
tin atom  (ISO)
tin(0)  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)

References

References - curated
1. Caccamo A, etal., Mol Neurodegener. 2010 Nov 11;5:51.
2. Casafont I, etal., J Struct Biol. 2009 Sep;167(3):235-41. Epub 2009 Jun 16.
3. Dasuri K, etal., J Neurosci Res. 2011 Sep;89(9):1471-7. doi: 10.1002/jnr.22677. Epub 2011 May 23.
4. Dayton RD, etal., Exp Neurol. 2011 Dec 9.
5. Dominguez V, etal., J Biol Chem. 2011 Feb 11;286(6):4216-25. doi: 10.1074/jbc.M110.200295. Epub 2010 Dec 2.
6. Freeman SH, etal., J Neuropathol Exp Neurol. 2008 Jan;67(1):62-7.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Gitcho MA, etal., Ann Neurol. 2008 Apr;63(4):535-8.
9. GOA data from the GO Consortium
10. Herman AM, etal., Brain Res. 2011 Apr 22;1386:191-9. Epub 2011 Mar 2.
11. Johnson VE, etal., Acta Neuropathol. 2011 Dec;122(6):715-26. Epub 2011 Nov 19.
12. Kabashi E, etal., Nat Genet. 2008 May;40(5):572-4. Epub 2008 Mar 30.
13. Kokoulina P and Rohn TT, Neurodegener Dis. 2010;7(4):243-50. Epub 2010 May 5.
14. McKee AC, etal., J Neuropathol Exp Neurol. 2010 Sep;69(9):918-29.
15. Nardo G, etal., PLoS One. 2011;6(10):e25545. Epub 2011 Oct 5.
16. Neumann M, etal., Science. 2006 Oct 6;314(5796):130-3.
17. OMIM Disease Annotation Pipeline
18. Piaceri I, etal., Clin Genet. 2011 Jun 8. doi: 10.1111/j.1399-0004.2011.01726.x.
19. Quadri M, etal., Neurogenetics. 2011 Aug;12(3):203-9. Epub 2011 Jun 11.
20. RGD automated data pipeline
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. Sephton CF, etal., J Biol Chem. 2011 Jan 14;286(2):1204-15. doi: 10.1074/jbc.M110.190884. Epub 2010 Nov 4.
24. Sreedharan J, etal., Science. 2008 Mar 21;319(5870):1668-72. Epub 2008 Feb 28.
25. Swarup V, etal., Brain. 2011 Sep;134(Pt 9):2610-26. Epub 2011 Jul 13.
26. Tremblay C, etal., J Neuropathol Exp Neurol. 2011 Sep;70(9):788-98.
27. Tsai KJ, etal., J Exp Med. 2010 Aug 2;207(8):1661-73. Epub 2010 Jul 26.
28. Yokota O, etal., Acta Neuropathol. 2010 Dec;120(6):789-801. Epub 2010 Jul 29.
29. Yokota O, etal., Acta Neuropathol. 2010 Jul;120(1):55-66. Epub 2010 May 30.
Additional References at PubMed
PMID:7745706   PMID:8889548   PMID:11285240   PMID:12477932   PMID:12947022   PMID:17481916   PMID:18305152   PMID:18836447   PMID:19383787   PMID:21666678   PMID:21700703   PMID:22082260  
PMID:22193716   PMID:22235134   PMID:22658674   PMID:22681889   PMID:22957047   PMID:23258539   PMID:23384725   PMID:23714777   PMID:23827948   PMID:24447103   PMID:24625528   PMID:24647938  
PMID:24917042   PMID:25002582   PMID:26099433   PMID:26735904   PMID:26887947   PMID:27123980   PMID:27378374   PMID:27735996   PMID:28265061   PMID:28335005   PMID:28585542   PMID:29313467  
PMID:29531287   PMID:29545601   PMID:31176717   PMID:31229690  


Genomics

Comparative Map Data
Tardbp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.05165,432,089 - 165,442,232 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5165,432,095 - 165,442,048 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05169,088,684 - 169,099,216 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45165,698,665 - 165,709,531 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15165,708,851 - 165,719,708 (-)NCBI
Celera5157,327,910 - 157,337,955 (-)NCBICelera
Cytogenetic Map5q36NCBI
TARDBP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl111,012,344 - 11,026,420 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl111,012,662 - 11,030,528 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl111,012,344 - 11,025,739 (+)EnsemblGRCh38hg38GRCh38
GRCh38111,012,654 - 11,030,528 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37111,072,462 - 11,085,549 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36110,995,266 - 11,008,136 (+)NCBINCBI36hg18NCBI36
Build 34111,006,944 - 11,019,814NCBI
Celera110,184,976 - 10,197,861 (+)NCBI
Cytogenetic Map1p36.22NCBI
HuRef110,224,341 - 10,237,229 (+)NCBIHuRef
CHM1_1111,060,321 - 11,073,209 (+)NCBICHM1_1
Tardbp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394148,696,839 - 148,711,672 (-)NCBI
GRCm384148,612,382 - 148,627,084 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4148,612,382 - 148,627,019 (-)EnsemblGRCm38mm10GRCm38
MGSCv374147,986,491 - 148,001,105 (-)NCBIGRCm37mm9NCBIm37
MGSCv364147,454,416 - 147,470,796 (-)NCBImm8
Celera4150,873,662 - 150,888,313 (-)NCBICelera
Cytogenetic Map4E2NCBI
Tardbp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554862,656,121 - 2,674,807 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554862,656,121 - 2,674,808 (-)NCBIChiLan1.0ChiLan1.0
TARDBP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1110,996,006 - 11,008,732 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl110,996,006 - 11,008,732 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v019,775,084 - 9,786,710 (+)NCBIMhudiblu_PPA_v0panPan3
TARDBP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl284,989,952 - 84,998,593 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1284,987,752 - 84,998,136 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tardbp
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647490,813 - 103,713 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TARDBP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl671,213,852 - 71,227,704 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1671,213,584 - 71,227,707 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2665,135,826 - 65,147,430 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TARDBP
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120120,753,764 - 120,765,259 (-)NCBI
Tardbp
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248181,759,496 - 1,789,806 (-)NCBI

Position Markers
HSC11D022  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05165,432,255 - 165,432,536NCBIRnor6.0
Rnor_5.05169,088,856 - 169,089,137UniSTSRnor5.0
RGSC_v3.45165,698,824 - 165,699,105UniSTSRGSC3.4
Celera5157,328,069 - 157,328,350UniSTS
Cytogenetic Map5q36UniSTS
UniSTS:479044  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05165,432,687 - 165,433,228NCBIRnor6.0
Rnor_5.05169,089,288 - 169,089,829UniSTSRnor5.0
RGSC_v3.45165,699,256 - 165,699,797UniSTSRGSC3.4
Celera5157,328,501 - 157,329,042UniSTS
Cytogenetic Map5q36UniSTS


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:35
Count of miRNA genes:33
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000049822
Prediction methods: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 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001011979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239384 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239385 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239386 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764235 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_354411 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_354412 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_354413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07050449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040811 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040812 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI502405 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC083752 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CF109817 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DV725863 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000049822   ⟹   ENSRNOP00000041889
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5165,432,095 - 165,442,048 (-)Ensembl
RefSeq Acc Id: NM_001011979   ⟹   NP_001011979
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05165,432,096 - 165,442,059 (-)NCBI
Rnor_5.05169,088,684 - 169,099,216 (-)NCBI
RGSC_v3.45165,698,665 - 165,709,531 (-)RGD
Celera5157,327,910 - 157,337,955 (-)RGD
Sequence:
RefSeq Acc Id: XM_006239382   ⟹   XP_006239444
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05165,432,233 - 165,442,232 (-)NCBI
Rnor_5.05169,088,684 - 169,099,216 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006239384   ⟹   XP_006239446
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05165,432,233 - 165,442,116 (-)NCBI
Rnor_5.05169,088,684 - 169,099,216 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006239385   ⟹   XP_006239447
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05165,432,233 - 165,442,216 (-)NCBI
Rnor_5.05169,088,684 - 169,099,216 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006239386   ⟹   XP_006239448
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05165,432,233 - 165,442,217 (-)NCBI
Rnor_5.05169,088,684 - 169,099,216 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764234   ⟹   XP_008762456
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05165,432,233 - 165,442,217 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764235   ⟹   XP_008762457
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05165,432,233 - 165,442,117 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764236   ⟹   XP_008762458
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05165,432,233 - 165,442,115 (-)NCBI
Sequence:
RefSeq Acc Id: XR_354411
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05165,432,089 - 165,442,232 (-)NCBI
Rnor_5.05169,088,684 - 169,099,216 (-)NCBI
Sequence:
RefSeq Acc Id: XR_354412
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05165,432,089 - 165,442,115 (-)NCBI
Rnor_5.05169,088,684 - 169,099,216 (-)NCBI
Sequence:
RefSeq Acc Id: XR_354413
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05165,432,089 - 165,442,216 (-)NCBI
Rnor_5.05169,088,684 - 169,099,216 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001011979   ⟸   NM_001011979
- UniProtKB: I6L9G6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239447   ⟸   XM_006239385
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006239448   ⟸   XM_006239386
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006239446   ⟸   XM_006239384
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006239444   ⟸   XM_006239382
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008762456   ⟸   XM_008764234
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008762458   ⟸   XM_008764236
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_008762457   ⟸   XM_008764235
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000041889   ⟸   ENSRNOT00000049822
Protein Domains
RRM

Transcriptome

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

Promoters
RGD ID:13694266
Promoter ID:EPDNEW_R4790
Type:multiple initiation site
Name:Tardbp_1
Description:TAR DNA binding protein
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_6.05165,442,055 - 165,442,115EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/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)
ACI/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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 169091272 169091273 T G snv BUF/MNa (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310906 AgrOrtholog
Ensembl Genes ENSRNOG00000012455 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000041889 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000049822 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7192591 IMAGE-MGC_LOAD
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RRM_RNP1 UniProtKB/TrEMBL
  TDP43_N UniProtKB/TrEMBL
KEGG Report rno:298648 UniProtKB/TrEMBL
MGC_CLONE MGC:94685 IMAGE-MGC_LOAD
NCBI Gene 298648 ENTREZGENE
Pfam RRM_1 UniProtKB/TrEMBL
  TDP43_N UniProtKB/TrEMBL
PhenoGen Tardbp PhenoGen
PROSITE RRM UniProtKB/TrEMBL
SMART RRM UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniGene Rn.2633 ENTREZGENE
UniProt I6L9G6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Tardbp  TAR DNA binding protein  Tardbp_predicted  TAR DNA binding protein (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tardbp_predicted  TAR DNA binding protein (predicted)      Symbol and Name status set to approved 70820 APPROVED