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: Enables RNA binding activity. Involved in positive regulation of insulin secretion and response to endoplasmic reticulum stress. Located in interchromatin granule; nuclear speck; and perichromatin fibrils. 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 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC298648; TAR DNA-binding protein 43; Tdp-43
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85164,330,452 - 164,348,435 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5164,334,924 - 164,345,204 (-)EnsemblGRCr8
mRatBN7.25159,050,518 - 159,062,218 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5159,051,799 - 159,062,055 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5161,768,493 - 161,778,784 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05163,590,953 - 163,601,242 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05163,547,298 - 163,557,588 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05165,432,089 - 165,442,232 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5165,432,095 - 165,442,048 (-)Ensemblrn6Rnor6.0
Rnor_5.05169,088,684 - 169,099,216 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45165,698,665 - 165,709,531 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5157,327,910 - 157,337,955 (-)NCBICelera
RGSC_v3.15165,708,851 - 165,719,708 (-)NCBI
Cytogenetic Map5q36NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-tribromophenol  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3',5'-cyclic UMP  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
aconitine  (EXP)
acrolein  (ISO)
alpha-pinene  (ISO)
alpha-Zearalanol  (EXP)
amitrole  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antimony(0)  (ISO)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-lapachone  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol AF  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bufalin  (ISO)
butanal  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
cannabidiol  (ISO)
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)
D-glucitol  (ISO)
DDE  (ISO)
decabromodiphenyl ether  (ISO)
diallyl trisulfide  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
digoxin  (ISO)
dioxygen  (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)
hexachlorophene  (ISO)
hydrogen cyanide  (ISO)
hydroquinone  (ISO)
hydroquinone O-beta-D-glucopyranoside  (ISO)
irinotecan  (ISO)
ivermectin  (ISO)
L-serine  (EXP)
lanatoside C  (ISO)
lead(0)  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
mercury atom  (ISO)
mercury dichloride  (EXP)
mercury(0)  (ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
mono(2-ethylhexyl) phthalate  (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)
nitrates  (ISO)
nobiletin  (ISO)
Nonylphenol  (EXP)
ochratoxin A  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (EXP)
paraquat  (ISO)
pentanal  (ISO)
perfluorooctanoic acid  (EXP)
PF-670462  (ISO)
phenobarbital  (ISO)
phenol  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium cyanide  (ISO)
progesterone  (ISO)
Proscillaridin  (ISO)
pyocyanine  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
temozolomide  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
thiram  (ISO)
tin atom  (ISO)
tin(0)  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
Triptolide  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Age-dependent changes in TDP-43 levels in a mouse model of Alzheimer disease are linked to Abeta oligomers accumulation. Caccamo A, etal., Mol Neurodegener. 2010 Nov 11;5:51.
2. TDP-43 localizes in mRNA transcription and processing sites in mammalian neurons. Casafont I, etal., J Struct Biol. 2009 Sep;167(3):235-41. Epub 2009 Jun 16.
3. Amino acid analog toxicity in primary rat neuronal and astrocyte cultures: implications for protein misfolding and TDP-43 regulation. Dasuri K, etal., J Neurosci Res. 2011 Sep;89(9):1471-7. doi: 10.1002/jnr.22677. Epub 2011 May 23.
4. Frontotemporal lobar degeneration-related proteins induce only subtle memory-related deficits when bilaterally overexpressed in the dorsal hippocampus. Dayton RD, etal., Exp Neurol. 2011 Dec 9.
5. Class II phosphoinositide 3-kinase regulates exocytosis of insulin granules in pancreatic beta cells. Dominguez V, etal., J Biol Chem. 2011 Feb 11;286(6):4216-25. doi: 10.1074/jbc.M110.200295. Epub 2010 Dec 2.
6. TAR-DNA binding protein 43 in Pick disease. Freeman SH, etal., J Neuropathol Exp Neurol. 2008 Jan;67(1):62-7.
7. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. TDP-43 A315T mutation in familial motor neuron disease. Gitcho MA, etal., Ann Neurol. 2008 Apr;63(4):535-8.
9. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
10. beta-Amyloid triggers ALS-associated TDP-43 pathology in AD models. Herman AM, etal., Brain Res. 2011 Apr 22;1386:191-9. Epub 2011 Mar 2.
11. Acute and chronically increased immunoreactivity to phosphorylation-independent but not pathological TDP-43 after a single traumatic brain injury in humans. Johnson VE, etal., Acta Neuropathol. 2011 Dec;122(6):715-26. Epub 2011 Nov 19.
12. TARDBP mutations in individuals with sporadic and familial amyotrophic lateral sclerosis. Kabashi E, etal., Nat Genet. 2008 May;40(5):572-4. Epub 2008 Mar 30.
13. Caspase-cleaved transactivation response DNA-binding protein 43 in Parkinson's disease and dementia with Lewy bodies. Kokoulina P and Rohn TT, Neurodegener Dis. 2010;7(4):243-50. Epub 2010 May 5.
14. TDP-43 proteinopathy and motor neuron disease in chronic traumatic encephalopathy. McKee AC, etal., J Neuropathol Exp Neurol. 2010 Sep;69(9):918-29.
15. Amyotrophic lateral sclerosis multiprotein biomarkers in peripheral blood mononuclear cells. Nardo G, etal., PLoS One. 2011;6(10):e25545. Epub 2011 Oct 5.
16. Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Neumann M, etal., Science. 2006 Oct 6;314(5796):130-3.
17. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
18. TDP43/HDAC6/Prdx1 signaling pathway participated in the cognitive impairment of obstructive sleep apnea via regulating inflammation and oxidative stress. Ou Y, etal., Int Immunopharmacol. 2024 Jan 25;127:111350. doi: 10.1016/j.intimp.2023.111350. Epub 2023 Dec 17.
19. Clinical heterogeneity in Italian patients with amyotrophic lateral sclerosis. Piaceri I, etal., Clin Genet. 2011 Jun 8. doi: 10.1111/j.1399-0004.2011.01726.x.
20. Broadening the phenotype of TARDBP mutations: the TARDBP Ala382Thr mutation and Parkinson's disease in Sardinia. Quadri M, etal., Neurogenetics. 2011 Aug;12(3):203-9. Epub 2011 Jun 11.
21. GOA pipeline RGD automated data pipeline
22. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
23. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
24. Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. Sephton CF, etal., J Biol Chem. 2011 Jan 14;286(2):1204-15. doi: 10.1074/jbc.M110.190884. Epub 2010 Nov 4.
25. TDP-43 mutations in familial and sporadic amyotrophic lateral sclerosis. Sreedharan J, etal., Science. 2008 Mar 21;319(5870):1668-72. Epub 2008 Feb 28.
26. Pathological hallmarks of amyotrophic lateral sclerosis/frontotemporal lobar degeneration in transgenic mice produced with TDP-43 genomic fragments. Swarup V, etal., Brain. 2011 Sep;134(Pt 9):2610-26. Epub 2011 Jul 13.
27. Accumulation of transactive response DNA binding protein 43 in mild cognitive impairment and Alzheimer disease. Tremblay C, etal., J Neuropathol Exp Neurol. 2011 Sep;70(9):788-98.
28. Elevated expression of TDP-43 in the forebrain of mice is sufficient to cause neurological and pathological phenotypes mimicking FTLD-U. Tsai KJ, etal., J Exp Med. 2010 Aug 2;207(8):1661-73. Epub 2010 Jul 26.
29. Effect of topographical distribution of alpha-synuclein pathology on TDP-43 accumulation in Lewy body disease. Yokota O, etal., Acta Neuropathol. 2010 Dec;120(6):789-801. Epub 2010 Jul 29.
30. Phosphorylated TDP-43 pathology and hippocampal sclerosis in progressive supranuclear palsy. 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   PMID:32265469   PMID:37000196   PMID:38235539   PMID:38761845  


Genomics

Comparative Map Data
Tardbp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85164,330,452 - 164,348,435 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5164,334,924 - 164,345,204 (-)EnsemblGRCr8
mRatBN7.25159,050,518 - 159,062,218 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5159,051,799 - 159,062,055 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5161,768,493 - 161,778,784 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05163,590,953 - 163,601,242 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05163,547,298 - 163,557,588 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05165,432,089 - 165,442,232 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5165,432,095 - 165,442,048 (-)Ensemblrn6Rnor6.0
Rnor_5.05169,088,684 - 169,099,216 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45165,698,665 - 165,709,531 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5157,327,910 - 157,337,955 (-)NCBICelera
RGSC_v3.15165,708,851 - 165,719,708 (-)NCBI
Cytogenetic Map5q36NCBI
TARDBP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38111,012,654 - 11,030,528 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl111,012,344 - 11,030,528 (+)Ensemblhg38GRCh38
GRCh37111,072,711 - 11,085,549 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36110,995,266 - 11,008,136 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34111,006,944 - 11,019,814NCBI
Celera110,184,976 - 10,197,861 (+)NCBICelera
Cytogenetic Map1p36.22NCBI
HuRef110,224,341 - 10,237,229 (+)NCBIHuRef
CHM1_1111,060,321 - 11,073,209 (+)NCBICHM1_1
T2T-CHM13v2.0110,553,914 - 10,571,805 (+)NCBIT2T-CHM13v2.0
Tardbp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394148,696,839 - 148,711,672 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4148,696,839 - 148,711,476 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm384148,612,382 - 148,627,084 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4148,612,382 - 148,627,019 (-)Ensemblmm10GRCm38
MGSCv374147,986,491 - 148,001,105 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv364147,454,416 - 147,470,796 (-)NCBIMGSCv36mm8
Celera4150,873,662 - 150,888,313 (-)NCBICelera
Cytogenetic Map4E2NCBI
cM Map478.77NCBI
Tardbp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554862,656,121 - 2,674,807 (-)Ensembl
ChiLan1.0NW_0049554862,656,121 - 2,674,808 (-)NCBIChiLan1.0ChiLan1.0
TARDBP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21217,200,843 - 217,212,563 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11215,840,309 - 215,858,530 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v019,775,084 - 9,786,710 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1110,996,006 - 11,008,732 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl110,996,006 - 11,008,732 (+)EnsemblpanPan2panpan1.1
TARDBP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1284,987,752 - 84,998,136 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl284,989,952 - 84,998,593 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha281,515,040 - 81,527,435 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0285,647,107 - 85,659,313 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl285,649,924 - 85,659,763 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1282,395,167 - 82,407,547 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0283,396,611 - 83,408,986 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0284,459,460 - 84,471,855 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tardbp
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505834,266,198 - 34,278,928 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647491,037 - 100,280 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647490,813 - 103,713 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TARDBP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl671,213,860 - 71,227,704 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1671,213,584 - 71,227,707 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2665,135,826 - 65,147,430 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TARDBP
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120120,753,764 - 120,765,259 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605424,661,891 - 24,675,297 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tardbp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248181,759,497 - 1,789,813 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248181,759,496 - 1,789,806 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tardbp
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1112,147,816 - 12,157,865 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tardbp
35 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5130249266172190305Rat
1354583Despr3Despair related QTL34.980.0002locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)5132930505172190305Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5141212838172190305Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5149642129171146538Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5160111176171146538Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)599905133172190305Rat
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)5133789363172190305Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5134369199172190305Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)565089051166764498Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136631198172190305Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5156396728172190305Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133081618172190305Rat
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)551657967166600247Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138002522170842766Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5133270647172190305Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5160071170172129029Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)5141764300172190305Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5133789363172190305Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5148093485172129029Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5125969677172190305Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555124766172190305Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5156396728167181764Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5131708216172190305Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5149661912166600247Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5156289283171137955Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133081618172190305Rat

Markers in Region
HSC11D022  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25159,051,958 - 159,052,240 (+)MAPPERmRatBN7.2
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
mRatBN7.25159,052,390 - 159,052,932 (+)MAPPERmRatBN7.2
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


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
19 13 67 167 91 90 59 93 59 6 376 194 13 146 96 92 31 19 19

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001011979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001399105 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_174161 (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
  XM_039109697 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005504412 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010066364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010066365 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010066366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010066367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010066368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010066369 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010066370 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010066371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010066372 (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 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
  JAXUCZ010000005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000049822   ⟹   ENSRNOP00000041889
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5164,334,924 - 164,345,169 (-)Ensembl
mRatBN7.2 Ensembl5159,051,799 - 159,062,045 (-)Ensembl
Rnor_6.0 Ensembl5165,432,095 - 165,442,048 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000103485   ⟹   ENSRNOP00000095901
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5164,335,062 - 164,345,204 (-)Ensembl
mRatBN7.2 Ensembl5159,051,939 - 159,062,055 (-)Ensembl
RefSeq Acc Id: NM_001011979   ⟹   NP_001011979
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,335,062 - 164,345,204 (-)NCBI
mRatBN7.25159,051,937 - 159,062,080 (-)NCBI
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: NM_001399105   ⟹   NP_001386034
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,335,062 - 164,345,204 (-)NCBI
mRatBN7.25159,051,937 - 159,062,080 (-)NCBI
RefSeq Acc Id: NR_174161
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,912 - 164,345,204 (-)NCBI
mRatBN7.25159,051,787 - 159,062,080 (-)NCBI
RefSeq Acc Id: XM_006239384   ⟹   XP_006239446
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,345,361 (-)NCBI
mRatBN7.25159,051,937 - 159,062,207 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,345,361 (-)NCBI
mRatBN7.25159,051,937 - 159,062,207 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,335,064 - 164,345,361 (-)NCBI
mRatBN7.25159,051,937 - 159,062,209 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,335,064 - 164,345,361 (-)NCBI
mRatBN7.25159,051,937 - 159,062,208 (-)NCBI
Rnor_6.05165,432,233 - 165,442,217 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764235   ⟹   XP_008762457
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,335,064 - 164,345,361 (-)NCBI
mRatBN7.25159,051,937 - 159,062,206 (-)NCBI
Rnor_6.05165,432,233 - 165,442,117 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764236   ⟹   XP_008762458
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,335,064 - 164,348,435 (-)NCBI
mRatBN7.25159,051,937 - 159,062,205 (-)NCBI
Rnor_6.05165,432,233 - 165,442,115 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109697   ⟹   XP_038965625
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,344,893 (-)NCBI
mRatBN7.25159,051,937 - 159,061,655 (-)NCBI
RefSeq Acc Id: XM_063287481   ⟹   XP_063143551
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,335,064 - 164,344,957 (-)NCBI
RefSeq Acc Id: XM_063287482   ⟹   XP_063143552
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,335,064 - 164,344,960 (-)NCBI
RefSeq Acc Id: XR_005504412
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,345,361 (-)NCBI
mRatBN7.25159,050,518 - 159,062,208 (-)NCBI
RefSeq Acc Id: XR_010066364
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,330,452 - 164,348,435 (-)NCBI
RefSeq Acc Id: XR_010066365
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,344,893 (-)NCBI
RefSeq Acc Id: XR_010066366
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,330,452 - 164,345,361 (-)NCBI
RefSeq Acc Id: XR_010066367
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,344,960 (-)NCBI
RefSeq Acc Id: XR_010066368
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,344,920 (-)NCBI
RefSeq Acc Id: XR_010066369
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,345,361 (-)NCBI
RefSeq Acc Id: XR_010066370
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,345,361 (-)NCBI
RefSeq Acc Id: XR_010066371
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,344,960 (-)NCBI
RefSeq Acc Id: XR_010066372
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,344,777 (-)NCBI
RefSeq Acc Id: XR_354411
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,348,435 (-)NCBI
mRatBN7.25159,050,520 - 159,062,218 (-)NCBI
Rnor_6.05165,432,089 - 165,442,232 (-)NCBI
Rnor_5.05169,088,684 - 169,099,216 (-)NCBI
Sequence:
RefSeq Acc Id: XR_354412
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,348,435 (-)NCBI
mRatBN7.25159,050,520 - 159,062,207 (-)NCBI
Rnor_6.05165,432,089 - 165,442,115 (-)NCBI
Rnor_5.05169,088,684 - 169,099,216 (-)NCBI
Sequence:
RefSeq Acc Id: XR_354413
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,334,925 - 164,345,361 (-)NCBI
mRatBN7.25159,050,518 - 159,062,207 (-)NCBI
Rnor_6.05165,432,089 - 165,442,216 (-)NCBI
Rnor_5.05169,088,684 - 169,099,216 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001011979   ⟸   NM_001011979
- Peptide Label: isoform 2
- UniProtKB: I6L9G6 (UniProtKB/TrEMBL),   A6IU83 (UniProtKB/TrEMBL),   A6IU85 (UniProtKB/TrEMBL),   J9JIJ9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239447   ⟸   XM_006239385
- Peptide Label: isoform X4
- UniProtKB: A6IU81 (UniProtKB/TrEMBL),   A6IU85 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239448   ⟸   XM_006239386
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006239446   ⟸   XM_006239384
- Peptide Label: isoform X3
- UniProtKB: A6IU85 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008762456   ⟸   XM_008764234
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008762458   ⟸   XM_008764236
- Peptide Label: isoform X6
- UniProtKB: A6IU85 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008762457   ⟸   XM_008764235
- Peptide Label: isoform X5
- UniProtKB: A6IU85 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000041889   ⟸   ENSRNOT00000049822
RefSeq Acc Id: XP_038965625   ⟸   XM_039109697
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GLU8 (UniProtKB/TrEMBL),   A6IU84 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000095901   ⟸   ENSRNOT00000103485
RefSeq Acc Id: NP_001386034   ⟸   NM_001399105
- Peptide Label: isoform 1
- UniProtKB: A0A8I6GLU8 (UniProtKB/TrEMBL),   A6IU84 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063143552   ⟸   XM_063287482
- Peptide Label: isoform X6
- UniProtKB: A6IU85 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063143551   ⟸   XM_063287481
- Peptide Label: isoform X3
- UniProtKB: A6IU85 (UniProtKB/TrEMBL)
Protein Domains
RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-I6L9G6-F1-model_v2 AlphaFold I6L9G6 1-285 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310906 AgrOrtholog
BioCyc Gene G2FUF-39158 BioCyc
Ensembl Genes ENSRNOG00000012455 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000049822 ENTREZGENE
  ENSRNOT00000049822.5 UniProtKB/TrEMBL
  ENSRNOT00000103485 ENTREZGENE
  ENSRNOT00000103485.2 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
  TDP-43_C UniProtKB/TrEMBL
  TDP43_N UniProtKB/TrEMBL
KEGG Report rno:298648 UniProtKB/TrEMBL
MGC_CLONE MGC:94685 IMAGE-MGC_LOAD
NCBI Gene 298648 ENTREZGENE
PANTHER RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN UniProtKB/TrEMBL
  TAR DNA-BINDING PROTEIN 43 UniProtKB/TrEMBL
Pfam RRM_1 UniProtKB/TrEMBL
  TDP-43_C UniProtKB/TrEMBL
  TDP43_N UniProtKB/TrEMBL
PhenoGen Tardbp PhenoGen
PROSITE RRM UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012455 RatGTEx
SMART RRM UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A0A8I6GLU8 ENTREZGENE, UniProtKB/TrEMBL
  A6IU81 ENTREZGENE, UniProtKB/TrEMBL
  A6IU83 ENTREZGENE, UniProtKB/TrEMBL
  A6IU84 ENTREZGENE, UniProtKB/TrEMBL
  A6IU85 ENTREZGENE, UniProtKB/TrEMBL
  I6L9G6 ENTREZGENE
  J9JIJ9 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary I6L9G6 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