Tsc1 (TSC complex subunit 1) - Rat Genome Database

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Gene: Tsc1 (TSC complex subunit 1) Rattus norvegicus
Analyze
Symbol: Tsc1
Name: TSC complex subunit 1
RGD ID: 620124
Description: Predicted to enable ATPase inhibitor activity; heat shock protein binding activity; and protein folding chaperone. Involved in several processes, including negative regulation of cellular response to oxidative stress; positive regulation of stress fiber assembly; and regulation of macroautophagy. Located in growth cone; nucleus; and perinuclear region of cytoplasm. Used to study obesity. Human ortholog(s) of this gene implicated in intellectual disability; lymphangioleiomyomatosis; tuberous sclerosis; and tuberous sclerosis 1. Orthologous to human TSC1 (TSC complex subunit 1); PARTICIPATES IN adenosine monophosphate-activated protein kinase (AMPK) signaling pathway; mTOR signaling pathway; insulin signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; aflatoxin B1; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hamartin; tuberous sclerosis 1; tuberous sclerosis 1 protein homolog
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
GRCr8332,367,434 - 32,416,565 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl332,367,670 - 32,416,568 (+)EnsemblGRCr8
mRatBN7.2311,969,547 - 12,018,591 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl311,979,729 - 12,015,674 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx315,059,218 - 15,086,859 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0323,644,177 - 23,671,817 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0321,898,622 - 21,926,266 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.037,219,955 - 7,269,063 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,237,192 - 7,265,145 (+)Ensemblrn6Rnor6.0
Rnor_5.0312,570,765 - 12,619,753 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.437,645,313 - 7,672,944 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera36,767,562 - 6,795,193 (+)NCBICelera
RGSC_v3.137,645,612 - 7,673,244 (+)NCBI
Cytogenetic Map3p12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
(S)-naringenin  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
acrolein  (ISO)
acrylamide  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
antroquinonol  (ISO)
atrazine  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium atom  (EXP)
cadmium dichloride  (EXP)
caffeine  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
Dibutyl phosphate  (ISO)
diclofenac  (ISO)
dieldrin  (EXP,ISO)
dorsomorphin  (EXP)
doxorubicin  (ISO)
folic acid  (ISO)
FR900359  (ISO)
furan  (EXP)
gentamycin  (EXP)
glyphosate  (ISO)
GSK-J4  (ISO)
hydrogen peroxide  (ISO)
hydroquinone O-beta-D-glucopyranoside  (ISO)
lead diacetate  (ISO)
linuron  (EXP)
liraglutide  (EXP)
methylmercury chloride  (ISO)
nickel atom  (ISO)
Nonylphenol  (EXP)
ozone  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
sirolimus  (ISO)
sodium arsenite  (EXP,ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
testosterone  (ISO)
thiram  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of GTPase activity  (ISO)
adaptive immune response  (ISO)
adult locomotory behavior  (IMP)
associative learning  (IEA,ISO)
cardiac muscle cell differentiation  (ISO)
cell projection organization  (ISO)
cell-matrix adhesion  (IEA,ISO)
cellular response to decreased oxygen levels  (IMP)
cellular response to starvation  (IEA,ISO,ISS)
cerebral cortex development  (ISO)
D-glucose import  (ISO)
hippocampus development  (ISO)
kidney development  (ISO)
memory T cell differentiation  (ISO)
myelination  (ISO)
negative regulation of ATP-dependent activity  (ISO)
negative regulation of cell population proliferation  (IBA,IEA,IMP,ISO)
negative regulation of cell size  (ISO)
negative regulation of cellular response to oxidative stress  (IMP)
negative regulation of GTPase activity  (IMP)
negative regulation of macroautophagy  (IMP)
negative regulation of neuron projection development  (IMP)
negative regulation of TOR signaling  (IBA,IEA,IMP,ISO)
negative regulation of TORC1 signaling  (IEA,ISO,ISS)
nervous system development  (ISO)
neural tube closure  (ISO)
positive regulation of focal adhesion assembly  (IEA,ISO)
positive regulation of macroautophagy  (IDA)
positive regulation of stress fiber assembly  (IMP)
potassium ion transport  (ISO)
protein folding  (IEA)
protein stabilization  (IEA,ISO)
regulation of cell cycle  (IBA)
regulation of cell-matrix adhesion  (IEA,ISO)
regulation of focal adhesion assembly  (IMP)
regulation of protein kinase activity  (ISO)
regulation of stress fiber assembly  (IEA,ISO)
response to insulin  (IEA,ISO)
response to nutrient levels  (IEP)
response to peptide  (IEP)
synapse organization  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Regulation of mTORC1 by PI3K signaling. Dibble CC and Cantley LC, Trends Cell Biol. 2015 Sep;25(9):545-55. doi: 10.1016/j.tcb.2015.06.002. Epub 2015 Jul 6.
2. Neurogenin 3-directed cre deletion of Tsc1 gene causes pancreatic acinar carcinoma. Ding L, etal., Neoplasia. 2014 Nov 20;16(11):909-17. doi: 10.1016/j.neo.2014.08.010. eCollection 2014 Nov.
3. Single-cell Tsc1 knockout during corticogenesis generates tuber-like lesions and reduces seizure threshold in mice. Feliciano DM, etal., J Clin Invest. 2011 Apr;121(4):1596-607. doi: 10.1172/JCI44909. Epub 2011 Mar 14.
4. Antisense suppression of TSC1 gene product, hamartin, enhances neurite outgrowth in NGF-treated PC12h cells. Floricel F, etal., Brain Dev. 2007 Sep;29(8):502-9. Epub 2007 Mar 21.
5. 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.
6. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
7. TSC2 modulates actin cytoskeleton and focal adhesion through TSC1-binding domain and the Rac1 GTPase. Goncharova E, etal., J Cell Biol. 2004 Dec 20;167(6):1171-82.
8. The TSC1 tumor suppressor hamartin interacts with neurofilament-L and possibly functions as a novel integrator of the neuronal cytoskeleton. Haddad LA, etal., J Biol Chem 2002 Nov 15;277(46):44180-6.
9. The preventive effect of liraglutide on the lipotoxic liver injury via increasing autophagy. He Y, etal., Ann Hepatol. 2020 Jan - Feb;19(1):44-52. doi: 10.1016/j.aohep.2019.06.023. Epub 2019 Sep 24.
10. GADD34 mediates cytoprotective autophagy in mutant huntingtin expressing cells via the mTOR pathway. Hyrskyluoto A, etal., Exp Cell Res. 2012 Jan 1;318(1):33-42. doi: 10.1016/j.yexcr.2011.08.020. Epub 2011 Sep 7.
11. Tuberin and hamartin are aberrantly expressed and linked to clinical outcome in human breast cancer: the role of promoter methylation of TSC genes. Jiang WG, etal., Eur J Cancer. 2005 Jul;41(11):1628-36.
12. A germ-line Tsc1 mutation causes tumor development and embryonic lethality that are similar, but not identical to, those caused by Tsc2 mutation in mice. Kobayashi T, etal., Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8762-7. Epub 2001 Jul 3.
13. TSC1 loss synergizes with KRAS activation in lung cancer development in the mouse and confers rapamycin sensitivity. Liang MC, etal., Oncogene. 2010 Mar 18;29(11):1588-97. doi: 10.1038/onc.2009.452. Epub 2009 Dec 7.
14. Molecular mechanisms of mTOR-mediated translational control. Ma XM and Blenis J, Nat Rev Mol Cell Biol. 2009 May;10(5):307-18. Epub 2009 Apr 2.
15. The tuberin-hamartin complex negatively regulates beta-catenin signaling activity. Mak BC, etal., J Biol Chem 2003 Feb 21;278(8):5947-51. Epub 2003 Jan 02.
16. Role of insulin, adipocyte hormones, and nutrient-sensing pathways in regulating fuel metabolism and energy homeostasis: a nutritional perspective of diabetes, obesity, and cancer. Marshall S Sci STKE. 2006 Aug 1;2006(346):re7.
17. N-terminal hamartin-binding and C-terminal GAP domain of tuberin can separate in vivo. Momose S, etal., Biochem Biophys Res Commun. 2007 May 11;356(3):693-8. Epub 2007 Mar 13.
18. Pam and its ortholog highwire interact with and may negatively regulate the TSC1.TSC2 complex. Murthy V, etal., J Biol Chem 2004 Jan 9;279(2):1351-8. Epub 2003 Oct 14.
19. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
20. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
21. Tsc1 (hamartin) confers neuroprotection against ischemia by inducing autophagy. Papadakis M, etal., Nat Med. 2013 Mar;19(3):351-7. doi: 10.1038/nm.3097. Epub 2013 Feb 24.
22. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
23. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
24. Survival benefit and phenotypic improvement by hamartin gene therapy in a tuberous sclerosis mouse brain model. Prabhakar S, etal., Neurobiol Dis. 2015 Oct;82:22-31. doi: 10.1016/j.nbd.2015.04.018. Epub 2015 May 24.
25. Analysis of 65 tuberous sclerosis complex (TSC) patients by TSC2 DGGE, TSC1/TSC2 MLPA, and TSC1 long-range PCR sequencing, and report of 28 novel mutations. Rendtorff ND, etal., Hum Mutat. 2005 Oct;26(4):374-83.
26. GOA pipeline RGD automated data pipeline
27. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
29. Inappropriate activation of the TSC/Rheb/mTOR/S6K cassette induces IRS1/2 depletion, insulin resistance, and cell survival deficiencies. Shah OJ, etal., Curr Biol. 2004 Sep 21;14(18):1650-6.
30. Identification of the tuberous sclerosis gene TSC1 on chromosome 9q34. van Slegtenhorst M, etal., Science. 1997 Aug 8;277(5327):805-8.
31. Frequent loss of chromosome 9, homozygous CDKN2A/p14(ARF)/CDKN2B deletion and low TSC1 mRNA expression in pleomorphic xanthoastrocytomas. Weber RG, etal., Oncogene. 2007 Feb 15;26(7):1088-97. Epub 2006 Aug 7.
32. Intellectual ability in tuberous sclerosis complex correlates with predicted effects of mutations on TSC1 and TSC2 proteins. Wong HT, etal., J Med Genet. 2015 Dec;52(12):815-22. doi: 10.1136/jmedgenet-2015-103154. Epub 2015 Sep 25.
33. Multicompartmental distribution of the tuberous sclerosis gene products, hamartin and tuberin. Yamamoto Y, etal., Arch Biochem Biophys. 2002 Aug 15;404(2):210-7.
34. The TSC1 gene product hamartin interacts with NADE. Yasui S, etal., Mol Cell Neurosci. 2007 May;35(1):100-8. Epub 2007 Feb 12.
35. [Tsc1 promoter methylation rate, mTOR expression in food-induced obese rat hypothalamus]. Zhang L, etal., Sichuan Da Xue Xue Bao Yi Xue Ban. 2015 Jan;46(1):47-50.
36. TSC1 R509X Mutation in a Chinese Family with Tuberous Sclerosis Complex. Zhang Y, etal., Neuromolecular Med. 2015 Jun;17(2):202-8. doi: 10.1007/s12017-015-8354-x. Epub 2015 Apr 22.
Additional References at PubMed
PMID:9580671   PMID:9809973   PMID:10029074   PMID:10585443   PMID:10806479   PMID:10807585   PMID:10915759   PMID:11175345   PMID:11741832   PMID:15185396   PMID:15664737   PMID:15851513  
PMID:15888477   PMID:16286931   PMID:16393152   PMID:16636147   PMID:16996505   PMID:17308101   PMID:17522300   PMID:18511518   PMID:19348060   PMID:19420259   PMID:19897899   PMID:25211037  
PMID:25271321   PMID:28215400   PMID:29127155   PMID:32739207   PMID:37020385   PMID:39169069  


Genomics

Comparative Map Data
Tsc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8332,367,434 - 32,416,565 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl332,367,670 - 32,416,568 (+)EnsemblGRCr8
mRatBN7.2311,969,547 - 12,018,591 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl311,979,729 - 12,015,674 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx315,059,218 - 15,086,859 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0323,644,177 - 23,671,817 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0321,898,622 - 21,926,266 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.037,219,955 - 7,269,063 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,237,192 - 7,265,145 (+)Ensemblrn6Rnor6.0
Rnor_5.0312,570,765 - 12,619,753 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.437,645,313 - 7,672,944 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera36,767,562 - 6,795,193 (+)NCBICelera
RGSC_v3.137,645,612 - 7,673,244 (+)NCBI
Cytogenetic Map3p12NCBI
TSC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389132,891,349 - 132,945,378 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9132,891,348 - 132,946,874 (-)Ensemblhg38GRCh38
GRCh379135,766,736 - 135,820,003 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369134,756,557 - 134,809,841 (-)NCBIBuild 36Build 36hg18NCBI36
Build 349132,815,940 - 132,849,574NCBI
Celera9106,308,473 - 106,361,761 (-)NCBICelera
Cytogenetic Map9q34.13NCBI
HuRef9105,260,658 - 105,313,711 (-)NCBIHuRef
CHM1_19135,917,213 - 135,970,447 (-)NCBICHM1_1
T2T-CHM13v2.09145,103,162 - 145,157,190 (-)NCBIT2T-CHM13v2.0
Tsc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39228,531,005 - 28,581,183 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl228,531,240 - 28,581,179 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38228,640,993 - 28,691,172 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl228,641,228 - 28,691,167 (+)Ensemblmm10GRCm38
MGSCv37228,496,763 - 28,546,687 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36228,463,252 - 28,513,176 (+)NCBIMGSCv36mm8
Celera228,345,749 - 28,395,673 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.38NCBI
Tsc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555132,197,037 - 2,244,992 (-)Ensembl
ChiLan1.0NW_0049555132,197,037 - 2,244,992 (-)NCBIChiLan1.0ChiLan1.0
TSC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2116,414,619 - 6,468,611 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan196,415,528 - 6,470,948 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09104,007,708 - 104,060,938 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19132,638,003 - 132,692,264 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9132,638,003 - 132,675,759 (-)EnsemblpanPan2panpan1.1
TSC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1951,409,307 - 51,459,546 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl951,425,937 - 51,454,677 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha950,673,940 - 50,724,548 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0952,304,134 - 52,354,724 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl952,304,753 - 52,354,693 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1951,082,516 - 51,133,112 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0951,407,015 - 51,457,594 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0951,486,514 - 51,537,117 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tsc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947199,562,656 - 199,618,374 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648719,331,194 - 19,386,892 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493648719,331,183 - 19,386,841 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TSC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1272,636,532 - 272,685,951 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11272,636,530 - 272,685,948 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21306,795,196 - 306,819,962 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TSC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1125,195,604 - 5,249,042 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl125,195,675 - 5,244,157 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607910,396,791 - 10,450,324 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tsc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247603,498,692 - 3,532,011 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247603,479,028 - 3,536,612 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Tsc1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v157,987,540 - 8,033,114 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tsc1
373 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:46
Count of miRNA genes:41
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000016904
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32905627547904329Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10450811Scl73Serum cholesterol level QTL 734.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat
10450808Scl72Serum cholesterol level QTL 724.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
10450806Scl71Serum cholesterol level QTL 715.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)32862533967641995Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)3612543751125437Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)33083238444921701Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3136721849Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3655634751556347Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31527234860272348Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)32905627547904329Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat

Markers in Region
PMC18172P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2311,991,703 - 11,992,226 (+)MAPPERmRatBN7.2
Rnor_6.037,242,180 - 7,242,702NCBIRnor6.0
Rnor_5.0312,592,870 - 12,593,392UniSTSRnor5.0
RGSC_v3.437,650,177 - 7,650,699UniSTSRGSC3.4
Celera36,772,426 - 6,772,948UniSTS
Cytogenetic Map3p12UniSTS


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
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_021854 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233844 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233845 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233846 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233849 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105772 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284467 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284468 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284469 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284474 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284476 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB011821 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB016165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC129847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000016904   ⟹   ENSRNOP00000016904
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl332,367,670 - 32,416,568 (+)Ensembl
mRatBN7.2 Ensembl311,979,729 - 12,015,674 (+)Ensembl
Rnor_6.0 Ensembl37,237,192 - 7,265,145 (+)Ensembl
RefSeq Acc Id: NM_021854   ⟹   NP_068626
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,367,697 - 32,416,562 (+)NCBI
mRatBN7.2311,969,725 - 12,018,588 (+)NCBI
Rnor_6.037,237,316 - 7,264,947 (+)NCBI
Rnor_5.0312,570,765 - 12,619,753 (+)NCBI
RGSC_v3.437,645,313 - 7,672,944 (+)RGD
Celera36,767,562 - 6,795,193 (+)RGD
Sequence:
RefSeq Acc Id: XM_006233844   ⟹   XP_006233906
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,367,434 - 32,416,565 (+)NCBI
mRatBN7.2311,969,549 - 12,018,591 (+)NCBI
Rnor_6.037,219,955 - 7,269,063 (+)NCBI
Rnor_5.0312,570,765 - 12,619,753 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233845   ⟹   XP_006233907
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,367,760 - 32,416,565 (+)NCBI
mRatBN7.2311,970,129 - 12,018,591 (+)NCBI
Rnor_6.037,220,597 - 7,269,063 (+)NCBI
Rnor_5.0312,570,765 - 12,619,753 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233846   ⟹   XP_006233908
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,375,074 - 32,416,565 (+)NCBI
mRatBN7.2311,978,921 - 12,018,591 (+)NCBI
Rnor_6.037,227,084 - 7,269,063 (+)NCBI
Rnor_5.0312,570,765 - 12,619,753 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233847   ⟹   XP_006233909
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,374,514 - 32,416,565 (+)NCBI
mRatBN7.2311,976,537 - 12,018,591 (+)NCBI
Rnor_6.037,227,013 - 7,269,063 (+)NCBI
Rnor_5.0312,570,765 - 12,619,753 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233849   ⟹   XP_006233911
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,367,522 - 32,416,565 (+)NCBI
mRatBN7.2311,969,547 - 12,018,591 (+)NCBI
Rnor_6.037,219,955 - 7,269,063 (+)NCBI
Rnor_5.0312,570,765 - 12,619,753 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039105772   ⟹   XP_038961700
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,374,633 - 32,416,565 (+)NCBI
mRatBN7.2311,976,662 - 12,018,591 (+)NCBI
RefSeq Acc Id: XM_063284467   ⟹   XP_063140537
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,367,518 - 32,416,565 (+)NCBI
RefSeq Acc Id: XM_063284468   ⟹   XP_063140538
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,367,518 - 32,416,565 (+)NCBI
RefSeq Acc Id: XM_063284469   ⟹   XP_063140539
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,374,512 - 32,416,565 (+)NCBI
RefSeq Acc Id: XM_063284470   ⟹   XP_063140540
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,368,138 - 32,416,565 (+)NCBI
RefSeq Acc Id: XM_063284471   ⟹   XP_063140541
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,375,070 - 32,416,565 (+)NCBI
RefSeq Acc Id: XM_063284472   ⟹   XP_063140542
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,367,806 - 32,416,565 (+)NCBI
RefSeq Acc Id: XM_063284474   ⟹   XP_063140544
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,367,516 - 32,416,565 (+)NCBI
RefSeq Acc Id: XM_063284475   ⟹   XP_063140545
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,367,792 - 32,416,565 (+)NCBI
RefSeq Acc Id: XM_063284476   ⟹   XP_063140546
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,367,522 - 32,416,565 (+)NCBI
RefSeq Acc Id: XM_063284477   ⟹   XP_063140547
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,387,250 - 32,416,565 (+)NCBI
RefSeq Acc Id: NP_068626   ⟸   NM_021854
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot),   A6JTP4 (UniProtKB/TrEMBL),   A0A8L2Q989 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233911   ⟸   XM_006233849
- Peptide Label: isoform X4
- UniProtKB: A0A8L2Q989 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233906   ⟸   XM_006233844
- Peptide Label: isoform X3
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot),   A6JTP4 (UniProtKB/TrEMBL),   A0A8L2Q989 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233907   ⟸   XM_006233845
- Peptide Label: isoform X3
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot),   A6JTP4 (UniProtKB/TrEMBL),   A0A8L2Q989 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233909   ⟸   XM_006233847
- Peptide Label: isoform X3
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot),   A6JTP4 (UniProtKB/TrEMBL),   A0A8L2Q989 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233908   ⟸   XM_006233846
- Peptide Label: isoform X3
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot),   A6JTP4 (UniProtKB/TrEMBL),   A0A8L2Q989 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000016904   ⟸   ENSRNOT00000016904
RefSeq Acc Id: XP_038961700   ⟸   XM_039105772
- Peptide Label: isoform X3
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot),   A6JTP4 (UniProtKB/TrEMBL),   A0A8L2Q989 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140544   ⟸   XM_063284474
- Peptide Label: isoform X2
- UniProtKB: A0A8L2Q989 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140537   ⟸   XM_063284467
- Peptide Label: isoform X1
- UniProtKB: A0A8L2Q989 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140538   ⟸   XM_063284468
- Peptide Label: isoform X1
- UniProtKB: A0A8L2Q989 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140546   ⟸   XM_063284476
- Peptide Label: isoform X4
- UniProtKB: A0A8L2Q989 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140545   ⟸   XM_063284475
- Peptide Label: isoform X3
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot),   A6JTP4 (UniProtKB/TrEMBL),   A0A8L2Q989 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140542   ⟸   XM_063284472
- Peptide Label: isoform X1
- UniProtKB: A0A8L2Q989 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140540   ⟸   XM_063284470
- Peptide Label: isoform X1
- UniProtKB: A0A8L2Q989 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140539   ⟸   XM_063284469
- Peptide Label: isoform X1
- UniProtKB: A0A8L2Q989 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140541   ⟸   XM_063284471
- Peptide Label: isoform X1
- UniProtKB: A0A8L2Q989 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140547   ⟸   XM_063284477
- Peptide Label: isoform X5
- UniProtKB: A0A8L2Q989 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9Z136-F1-model_v2 AlphaFold Q9Z136 1-1163 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620124 AgrOrtholog
BioCyc Gene G2FUF-50273 BioCyc
Ensembl Genes ENSRNOG00000011470 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000016904 ENTREZGENE
InterPro ARM-type_fold UniProtKB/Swiss-Prot
  Hamartin UniProtKB/Swiss-Prot
KEGG Report rno:60445 UniProtKB/Swiss-Prot
NCBI Gene 60445 ENTREZGENE
PANTHER HAMARTIN UniProtKB/Swiss-Prot
  PTHR15154 UniProtKB/Swiss-Prot
Pfam Hamartin UniProtKB/Swiss-Prot
PhenoGen Tsc1 PhenoGen
RatGTEx ENSRNOG00000011470 RatGTEx
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot
UniProt A0A8L2Q989 ENTREZGENE, UniProtKB/TrEMBL
  A6JTP4 ENTREZGENE, UniProtKB/TrEMBL
  Q9Z136 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-07-05 Tsc1  TSC complex subunit 1  Tsc1  tuberous sclerosis 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Tsc1  tuberous sclerosis 1      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Tsc1        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_function binds to neurofilament light chain 633519
gene_function associates with Pam, an interactor of Myc 1304444