Tsc1 (TSC complex subunit 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Tsc1 (TSC complex subunit 1) Rattus norvegicus
Analyze
Symbol: Tsc1
Name: TSC complex subunit 1
RGD ID: 620124
Description: Enables GTPase activating protein binding activity and protein N-terminus binding activity. Involved in several processes, including cellular response to oxygen-glucose deprivation; negative regulation of GTPase activity; and regulation of macroautophagy. Located in several cellular components, including cytosol; growth cone; and perinuclear region of cytoplasm. Part of protein-containing complex. 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: PROVISIONAL
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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2311,969,547 - 12,018,591 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl311,979,729 - 12,015,674 (+)Ensembl
Rnor_6.037,219,955 - 7,269,063 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,237,192 - 7,265,145 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0312,570,765 - 12,619,753 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.437,645,313 - 7,672,944 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.137,645,612 - 7,673,244 (+)NCBI
Celera36,767,562 - 6,795,193 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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  (ISO)
cardiac muscle cell differentiation  (ISO)
cell population proliferation  (ISO)
cell projection organization  (ISO)
cell-matrix adhesion  (ISO)
cellular response to oxygen-glucose deprivation  (IMP)
cerebral cortex development  (ISO)
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,IMP,ISO)
negative regulation of cell size  (ISO)
negative regulation of GTPase activity  (IMP)
negative regulation of macroautophagy  (IMP)
negative regulation of neuron projection development  (IMP)
negative regulation of oxidative stress-induced neuron death  (IMP)
negative regulation of TOR signaling  (IBA,IMP,ISO)
negative regulation of translation  (ISO)
nervous system development  (ISO)
neural tube closure  (ISO)
positive regulation of focal adhesion assembly  (ISO)
positive regulation of macroautophagy  (IDA)
positive regulation of stress fiber assembly  (IMP)
potassium ion transport  (ISO)
protein stabilization  (ISO)
regulation of cell cycle  (IBA)
regulation of cell-matrix adhesion  (ISO)
regulation of focal adhesion assembly  (IMP)
regulation of neuron death  (IMP)
regulation of phosphoprotein phosphatase activity  (ISO)
regulation of protein kinase activity  (ISO)
regulation of stress fiber assembly  (ISO)
regulation of translation  (ISO)
response to insulin  (ISO)
response to nutrient levels  (IEP)
response to peptide  (IEP)
rRNA export from nucleus  (ISO)
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  


Genomics

Comparative Map Data
Tsc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2311,969,547 - 12,018,591 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl311,979,729 - 12,015,674 (+)Ensembl
Rnor_6.037,219,955 - 7,269,063 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,237,192 - 7,265,145 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0312,570,765 - 12,619,753 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.437,645,313 - 7,672,944 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.137,645,612 - 7,673,244 (+)NCBI
Celera36,767,562 - 6,795,193 (+)NCBICelera
Cytogenetic Map3p12NCBI
TSC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389132,891,349 - 132,945,378 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl9132,891,348 - 132,946,874 (-)EnsemblGRCh38hg38GRCh38
GRCh379135,766,736 - 135,820,003 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369134,756,557 - 134,809,841 (-)NCBINCBI36hg18NCBI36
Build 349132,815,940 - 132,849,574NCBI
Celera9106,308,473 - 106,361,761 (-)NCBI
Cytogenetic Map9q34.13NCBI
HuRef9105,260,658 - 105,313,711 (-)NCBIHuRef
CHM1_19135,917,213 - 135,970,447 (-)NCBICHM1_1
T2T-CHM13v2.09145,103,162 - 145,156,431 (-)NCBI
Tsc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39228,531,005 - 28,581,184 (+)NCBIGRCm39mm39
GRCm39 Ensembl228,531,240 - 28,581,179 (+)Ensembl
GRCm38228,640,993 - 28,691,172 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl228,641,228 - 28,691,167 (+)EnsemblGRCm38mm10GRCm38
MGSCv37228,496,763 - 28,546,687 (+)NCBIGRCm37mm9NCBIm37
MGSCv36228,463,252 - 28,513,176 (+)NCBImm8
Celera228,345,749 - 28,395,673 (+)NCBICelera
Cytogenetic Map2A3NCBI
Tsc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555132,197,037 - 2,244,992 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555132,197,037 - 2,244,992 (-)NCBIChiLan1.0ChiLan1.0
TSC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19132,638,003 - 132,692,264 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9132,638,003 - 132,675,759 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09104,007,708 - 104,060,938 (-)NCBIMhudiblu_PPA_v0panPan3
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha950,673,940 - 50,724,548 (+)NCBI
ROS_Cfam_1.0952,304,134 - 52,354,724 (+)NCBI
ROS_Cfam_1.0 Ensembl952,304,753 - 52,354,693 (+)Ensembl
UMICH_Zoey_3.1951,082,516 - 51,133,112 (+)NCBI
UNSW_CanFamBas_1.0951,407,015 - 51,457,594 (+)NCBI
UU_Cfam_GSD_1.0951,486,514 - 51,537,117 (+)NCBI
Tsc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947199,562,656 - 199,618,374 (-)NCBI
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl125,195,675 - 5,244,157 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607910,396,791 - 10,450,324 (-)NCBIVero_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_1.0hetGla2
HetGla 1.0NW_0046247603,479,028 - 3,536,612 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat

miRNA Target Status

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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 26 14 4 17 4 3 74 28 40 11
Low 2 17 43 37 2 37 8 8 7 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016904   ⟹   ENSRNOP00000016904
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2311,986,840 - 12,014,471 (+)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_006233843   ⟹   XP_006233905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_006233844   ⟹   XP_006233906
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_017592016   ⟹   XP_017447505
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2311,989,278 - 12,018,591 (+)NCBI
Rnor_6.037,239,804 - 7,269,063 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039105772   ⟹   XP_038961700
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2311,976,662 - 12,018,591 (+)NCBI
RefSeq Acc Id: XM_039105773   ⟹   XP_038961701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2311,990,448 - 12,018,591 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_068626   ⟸   NM_021854
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233911   ⟸   XM_006233849
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006233905   ⟸   XM_006233843
- Peptide Label: isoform X1
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233906   ⟸   XM_006233844
- Peptide Label: isoform X1
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233907   ⟸   XM_006233845
- Peptide Label: isoform X1
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233909   ⟸   XM_006233847
- Peptide Label: isoform X1
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233908   ⟸   XM_006233846
- Peptide Label: isoform X1
- UniProtKB: Q9Z136 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017447505   ⟸   XM_017592016
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000016904   ⟸   ENSRNOT00000016904
RefSeq Acc Id: XP_038961700   ⟸   XM_039105772
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038961701   ⟸   XM_039105773
- Peptide Label: isoform X4

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620124 AgrOrtholog
BioCyc Gene G2FUF-50273 BioCyc
Ensembl Genes ENSRNOG00000011470 Ensembl, ENTREZGENE
Ensembl Protein ENSRNOP00000016904 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 PTHR15154 UniProtKB/Swiss-Prot
Pfam Hamartin UniProtKB/Swiss-Prot
PhenoGen Tsc1 PhenoGen
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot
UniProt 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