Snca (synuclein alpha) - Rat Genome Database

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Gene: Snca (synuclein alpha) Rattus norvegicus
Analyze
Symbol: Snca
Name: synuclein alpha
RGD ID: 3729
Description: Exhibits several functions, including phospholipase binding activity; protein N-terminus binding activity; and tubulin binding activity. Involved in several processes, including behavioral response to cocaine; negative regulation of nitrogen compound metabolic process; and response to desipramine. Localizes to several cellular components, including cytoplasmic vesicle; distal axon; and mitochondrion. Predicted to colocalize with platelet alpha granule membrane. Used to study Parkinson's disease and amphetamine abuse. Biomarker of mental depression and neurilemmoma. Human ortholog(s) of this gene implicated in Alzheimer's disease; Lewy body dementia; Parkinson's disease; Parkinson's disease 1; and Parkinson's disease 4. Orthologous to human SNCA (synuclein alpha); PARTICIPATES IN Parkinson's disease pathway; altered ubiquitin/proteasome degradation pathway; Alzheimer's disease pathway; INTERACTS WITH 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: alpha-synuclein; MGC105443; synuclein, alpha; synuclein, alpha (non A4 component of amyloid precursor); truncated alpha synuclein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   NP.P-(D4Rat119-D4Rat55)/Iusm   P/Iusm   NP/Iusm   P.NP-(Snca-D4Rat35)/Iusm  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2489,696,420 - 89,797,240 (-)NCBI
Rnor_6.0 Ensembl490,782,374 - 90,882,285 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0490,782,412 - 90,883,236 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04155,592,411 - 155,690,724 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4489,613,731 - 89,722,807 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1489,858,155 - 89,967,232 (-)NCBI
Celera484,478,545 - 84,578,894 (-)NCBICelera
Cytogenetic Map4q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-alpha-tocopherol  (ISO)
(-)-selegiline  (ISO)
(25R)-cholest-5-ene-3beta,26-diol  (ISO)
(3,4-dihydroxyphenyl)acetic acid  (ISO)
(R)-lipoic acid  (ISO)
(RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline  (ISO)
(S)-amphetamine  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (EXP,ISO)
1-nitropyrene  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-butoxyethanol  (ISO)
2-hydroxypropanoic acid  (ISO)
2-methylcholine  (ISO)
2-naphthylamine  (ISO)
26-hydroxycholesterol  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3-hydroxybutyric acid  (ISO)
3-methyladenine  (ISO)
3-phenylprop-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (ISO)
5,6,7,8-tetrahydrobiopterin  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
actinomycin D  (EXP)
alcohol  (ISO)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (EXP)
aluminium atom  (ISO)
aluminium(0)  (ISO)
ammonium chloride  (EXP,ISO)
anthocyanin  (ISO)
antirheumatic drug  (ISO)
apigenin  (EXP)
apocynin  (EXP)
aristolochic acid  (EXP)
Aroclor 1254  (EXP)
arsane  (ISO)
arsenic acid  (EXP)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
ATP  (ISO)
atrazine  (EXP)
bafilomycin A1  (ISO)
baicalein  (ISO)
BAPTA  (EXP)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
bortezomib  (ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
Calpeptin  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (EXP,ISO)
cis-caffeic acid  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
cocaine  (ISO)
coenzyme Q10  (EXP,ISO)
conduritol B epoxide  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (ISO)
Corynoxine B  (ISO)
creatine  (ISO)
curcumin  (ISO)
cyclosporin A  (EXP,ISO)
cypermethrin  (EXP,ISO)
cytarabine  (ISO)
dabigatran  (EXP)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibenziodolium  (ISO)
dibutyl phthalate  (ISO)
dichloroacetic acid  (ISO)
dichlorvos  (EXP)
diclofenac  (ISO)
dieldrin  (EXP,ISO)
diethyldithiocarbamic acid  (EXP)
diethylstilbestrol  (EXP)
dimethylarsinic acid  (EXP)
dioxygen  (ISO)
dopamine  (EXP,ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
echinacoside  (ISO)
entacapone  (ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
fenpyroximate  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
gallic acid  (ISO)
gamma-tocopherol  (ISO)
geraniol  (ISO)
glutathione  (EXP,ISO)
glutathione disulfide  (ISO)
glyburide  (ISO)
glyphosate  (ISO)
GTP  (EXP)
GW 3965  (ISO)
heptanal  (ISO)
hexanal  (ISO)
hydrogen peroxide  (EXP,ISO)
hydroxyurea  (ISO)
iron atom  (ISO)
iron dichloride  (ISO)
iron(0)  (ISO)
iron(2+) sulfate (anhydrous)  (ISO)
L-ascorbic acid  (ISO)
lactacystin  (EXP,ISO)
lead diacetate  (EXP)
lead nitrate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
linsidomine  (ISO)
lipoic acid  (ISO)
lipopolysaccharide  (ISO)
lithium atom  (EXP)
lithium chloride  (ISO)
lithium hydride  (EXP)
maneb  (ISO)
manganese atom  (EXP,ISO)
manganese(0)  (EXP,ISO)
manganese(II) chloride  (EXP,ISO)
melatonin  (EXP)
mercury dibromide  (ISO)
methamphetamine  (EXP,ISO)
methylmercury chloride  (ISO)
microcystin  (EXP)
morphine  (EXP)
N-acetyl-L-cysteine  (EXP,ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
nicotinic acid  (ISO)
nitric oxide  (ISO)
nonanal  (ISO)
O-acetyl-L-carnitine  (ISO)
octanal  (ISO)
omega-conotoxin GVIA  (EXP)
oxidopamine  (EXP,ISO)
paracetamol  (ISO)
paraquat  (ISO)
PCB138  (EXP)
pentanal  (ISO)
permethrin  (EXP,ISO)
phenobarbital  (ISO)
potassium dichromate  (ISO)
proanthocyanidin  (ISO)
probucol  (ISO)
propanal  (ISO)
pyridaben  (ISO)
pyrogallol  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
raloxifene  (EXP)
reactive nitrogen species  (ISO)
reactive oxygen species  (ISO)
reserpine  (ISO)
resveratrol  (ISO)
rifampicin  (EXP)
rotenone  (EXP,ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
sapropterin  (ISO)
sarin  (EXP,ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
sirolimus  (ISO)
SKF 38393  (EXP)
sodium arsenite  (EXP,ISO)
staurosporine  (ISO)
stigmatellin A  (ISO)
tacrine  (EXP)
tamoxifen  (ISO)
taurine  (ISO)
tauroursodeoxycholic acid  (ISO)
telmisartan  (ISO)
testosterone  (EXP)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
tocopherol  (ISO)
tolcapone  (ISO)
topotecan  (EXP)
trans-caffeic acid  (ISO)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
vitamin E  (ISO)
ziram  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
adult locomotory behavior  (ISO)
aging  (IEP)
apoptotic process  (IEA)
behavioral response to cocaine  (IMP)
calcium ion homeostasis  (ISO)
cellular response to copper ion  (ISO)
cellular response to fibroblast growth factor stimulus  (IEP)
cellular response to oxidative stress  (ISO)
chemical synaptic transmission  (IBA,ISO)
dopamine biosynthetic process  (ISO)
dopamine metabolic process  (ISO)
excitatory postsynaptic potential  (ISO)
fatty acid metabolic process  (ISO)
long-term synaptic potentiation  (ISO)
membrane organization  (ISO)
microglial cell activation  (ISO)
mitochondrial ATP synthesis coupled electron transport  (ISO)
mitochondrial membrane organization  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of chaperone-mediated autophagy  (ISO)
negative regulation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
negative regulation of dopamine metabolic process  (IMP)
negative regulation of dopamine uptake involved in synaptic transmission  (ISO)
negative regulation of exocytosis  (ISO)
negative regulation of histone acetylation  (ISO)
negative regulation of microtubule polymerization  (ISO)
negative regulation of monooxygenase activity  (ISO)
negative regulation of neuron apoptotic process  (IMP,ISO)
negative regulation of neuron death  (IMP,ISO)
negative regulation of norepinephrine uptake  (ISO)
negative regulation of platelet-derived growth factor receptor signaling pathway  (ISO)
negative regulation of protein phosphorylation  (IMP)
negative regulation of serotonin uptake  (ISO)
negative regulation of thrombin-activated receptor signaling pathway  (ISO)
negative regulation of transporter activity  (ISO)
neutral lipid metabolic process  (ISO)
phospholipid metabolic process  (ISO)
positive regulation of endocytosis  (ISO)
positive regulation of exocytosis  (ISO)
positive regulation of glutathione peroxidase activity  (ISO)
positive regulation of hydrogen peroxide catabolic process  (ISO)
positive regulation of inflammatory response  (ISO)
positive regulation of inositol phosphate biosynthetic process  (ISO)
positive regulation of neuron death  (ISO)
positive regulation of neurotransmitter secretion  (ISO)
positive regulation of peptidyl-serine phosphorylation  (ISO)
positive regulation of protein serine/threonine kinase activity  (ISO)
positive regulation of receptor recycling  (ISO)
positive regulation of release of sequestered calcium ion into cytosol  (ISO)
positive regulation of SNARE complex assembly  (ISO)
positive regulation of synaptic transmission  (ISO)
protein complex oligomerization  (ISO)
protein destabilization  (ISO)
protein tetramerization  (ISO)
receptor internalization  (ISO)
regulation of acyl-CoA biosynthetic process  (ISO)
regulation of dopamine secretion  (ISO)
regulation of glutamate secretion  (ISO)
regulation of locomotion  (ISO)
regulation of long-term neuronal synaptic plasticity  (ISO)
regulation of macrophage activation  (ISO)
regulation of neuron apoptotic process  (ISO)
regulation of neuron death  (IBA,IGI)
regulation of neuronal synaptic plasticity  (ISO)
regulation of neurotransmitter secretion  (ISO)
regulation of norepinephrine uptake  (ISO)
regulation of phospholipase activity  (ISO)
regulation of presynapse assembly  (ISO)
regulation of reactive oxygen species metabolic process  (ISO)
regulation of transmembrane transporter activity  (ISO)
response to cocaine  (IEP)
response to desipramine  (IEP)
response to drug  (ISO)
response to interferon-gamma  (ISO)
response to interleukin-1  (ISO)
response to iron(II) ion  (ISO)
response to lipopolysaccharide  (ISO)
response to magnesium ion  (ISO)
SNARE complex assembly  (ISO)
synapse organization  (IBA,ISO)
synaptic transmission, dopaminergic  (ISO)
synaptic vesicle endocytosis  (IBA,ISO)
synaptic vesicle exocytosis  (ISO)
synaptic vesicle priming  (ISO)
synaptic vesicle transport  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Abeliovich A, etal., Neuron 2000 Jan;25(1):239-52.
2. Adamczyk A, etal., J Physiol Pharmacol. 2005 Mar;56(1):29-37.
3. Ahn BH, etal., J Biol Chem. 2002 Apr 5;277(14):12334-42. Epub 2002 Jan 30.
4. Alim MA, etal., J Biol Chem. 2002 Jan 18;277(3):2112-7. Epub 2001 Nov 6.
5. Beilina A and Cookson MR, J Neurochem. 2015 Jul 30. doi: 10.1111/jnc.13266.
6. Bobela W, etal., Biomolecules. 2015 Oct 16;5(4):2675-700. doi: 10.3390/biom5042675.
7. Boyer F and Dreyer JL, Eur J Neurosci. 2007 Nov;26(10):2764-76.
8. Brenz Verca MS, etal., Eur J Neurosci. 2003 Oct;18(7):1923-38.
9. Ciechanover A and Brundin P, Neuron 2003 Oct 9;40(2):427-46.
10. Ding TT, etal., Biochemistry 2002 Aug 13;41(32):10209-17.
11. Feany MB and Bender WW, Nature 2000 Mar 23;404(6776):394-8.
12. Galvin JE, etal., Am J Pathol. 2000 Aug;157(2):361-8.
13. Galvin JE, etal., Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13450-5.
14. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
15. Ghee M, etal., J Neurochem. 2000 Nov;75(5):2221-4.
16. GOA data from the GO Consortium
17. Gorbatyuk OS, etal., Mol Ther. 2010 Aug;18(8):1450-7. doi: 10.1038/mt.2010.115. Epub 2010 Jun 15.
18. Gorbatyuk OS, etal., Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):763-8. doi: 10.1073/pnas.0711053105. Epub 2008 Jan 4.
19. Hunn BH, etal., Trends Neurosci. 2015 Mar;38(3):178-88. doi: 10.1016/j.tins.2014.12.009. Epub 2015 Jan 29.
20. Jeannotte AM, etal., Neuropsychopharmacology. 2009 Mar;34(4):987-98. Epub 2008 Sep 17.
21. Jeannotte AM, etal., Neurosci Lett. 2009 Dec 25;467(2):86-9. doi: 10.1016/j.neulet.2009.10.010. Epub 2009 Oct 8.
22. Jellinger KA Acta Neuropathol. 2009 Apr;117(4):423-7. Epub 2009 Feb 6.
23. Jin J, etal., Mol Cell Proteomics. 2007 May;6(5):845-59. Epub 2006 Jul 18.
24. Kahle PJ, etal., Am J Pathol. 2001 Dec;159(6):2215-25.
25. KEGG
26. Kholodilov NG, etal., J Neurochem 1999 Dec;73(6):2586-99.
27. Kim SJ, etal., J Biol Chem 2003 Oct 24;278(43):41890-9. Epub 2003 Aug 12.
28. Kruger R, etal., Nat Genet. 1998 Feb;18(2):106-8.
29. Lee HJ, etal., J Biol Chem. 2002 Jan 4;277(1):671-8. Epub 2001 Oct 25.
30. Leng Y and Chuang DM, J Neurosci. 2006 Jul 12;26(28):7502-12. doi: 10.1523/JNEUROSCI.0096-06.2006.
31. Li JY, etal., Neuroscience. 2002;113(2):463-78.
32. Liang T, etal., Proc Natl Acad Sci U S A 2003 Apr 15;100(8):4690-5.
33. Lindersson E, etal., J Biol Chem. 2005 Feb 18;280(7):5703-15. Epub 2004 Dec 7.
34. Liu G, etal., Neurosci Lett. 2009 May 1;454(3):187-92. doi: 10.1016/j.neulet.2009.02.056. Epub 2009 Feb 28.
35. Liu L, etal., PLoS One. 2014 Aug 4;9(8):e103948. doi: 10.1371/journal.pone.0103948. eCollection 2014.
36. Lo Bianco C, etal., Proc Natl Acad Sci U S A 2002 Aug 6;99(16):10813-8.
37. Maitta RW, etal., Am J Hematol. 2011 Feb;86(2):230-4. doi: 10.1002/ajh.21932.
38. Maroteaux L and Scheller RH, Brain Res Mol Brain Res 1991 Oct;11(3-4):335-43.
39. Maroteaux L, etal., J Neurosci 1988 Aug;8(8):2804-15.
40. Mash DC, etal., J Neurosci. 2003 Apr 1;23(7):2564-71.
41. Masliah E, etal., Proc Natl Acad Sci U S A 2001 Oct 9;98(21):12245-50. Epub 2001 Sep 25.
42. Masliah E, etal., Science 2000 Feb 18;287(5456):1265-9.
43. MGD data from the GO Consortium
44. Mollenhauer B, etal., Exp Neurol. 2008 Oct;213(2):315-25. doi: 10.1016/j.expneurol.2008.06.004. Epub 2008 Jun 14.
45. Monti B, etal., J Neurochem. 2007 Oct;103(2):518-30. Epub 2007 Jul 17.
46. Mori F, etal., Acta Neuropathol. 2002 Feb;103(2):145-51. Epub 2001 Oct 18.
47. Mori F, etal., Acta Neuropathol. 2002 Nov;104(5):455-61. Epub 2002 Jul 2.
48. Mukaetova-Ladinska EB, etal., Dement Geriatr Cogn Disord. 2008;26(1):32-42. Epub 2008 Jun 25.
49. Murphy DD, etal., J Neurosci 2000 May 1;20(9):3214-20.
50. Nakajima T, etal., Brain Res. 2005 Apr 8;1040(1-2):73-80.
51. NCBI rat LocusLink and RefSeq merged data July 26, 2002
52. Nishioka K, etal., Arch Neurol. 2010 Aug;67(8):970-5.
53. OMIM Disease Annotation Pipeline
54. Papachroni KK, etal., J Neurochem. 2007 May;101(3):749-56.
55. Perez RG, etal., J Neurosci. 2002 Apr 15;22(8):3090-9.
56. Pipeline to import KEGG annotations from KEGG into RGD
57. Polymeropoulos MH, etal., Science. 1997 Jun 27;276(5321):2045-7.
58. Quilty MC, etal., Exp Neurol 2003 Jul;182(1):195-207.
59. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
60. RGD automated import pipeline for gene-chemical interactions
61. Rideout HJ, etal., J Neurochem. 2003 Feb;84(4):803-13.
62. Robertson DC, etal., J Neurochem. 2004 Jun;89(5):1126-36.
63. Schlossmacher MG, etal., Am J Pathol. 2002 May;160(5):1655-67.
64. Skibinski G, etal., J Neurosci. 2014 Jan 8;34(2):418-33. doi: 10.1523/JNEUROSCI.2712-13.2014.
65. Surgucheva I, etal., J Neurosci Res. 2002 Apr 1;68(1):97-106.
66. Suzuki K, etal., Neuroreport. 2003 Mar 24;14(4):551-4.
67. Tehranian R, etal., J Neurochem. 2006 Nov;99(4):1188-96. Epub 2006 Sep 18.
68. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
69. Tu PH, etal., Ann Neurol. 1998 Sep;44(3):415-22.
70. Uryu K, etal., Exp Neurol. 2003 Nov;184(1):214-24.
71. Vivacqua G, etal., Neuroscience. 2009 Feb 18;158(4):1478-87. doi: 10.1016/j.neuroscience.2008.12.001. Epub 2008 Dec 7.
72. Wakabayashi K, etal., Acta Neuropathol. 2000 Jan;99(1):14-20.
73. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
74. Xu Z, etal., Synapse. 2005 Jan;55(1):45-51.
75. Yu S, etal., Neuroscience. 2007 Mar 16;145(2):539-55. doi: 10.1016/j.neuroscience.2006.12.028. Epub 2007 Feb 1.
Additional References at PubMed
PMID:8248242   PMID:10319874   PMID:10407019   PMID:10818098   PMID:10964942   PMID:10978144   PMID:11312271   PMID:11850416   PMID:11918289   PMID:11956199   PMID:12037467   PMID:12239163  
PMID:12388586   PMID:12406186   PMID:12408865   PMID:12477932   PMID:12787066   PMID:12958153   PMID:14507911   PMID:14645218   PMID:15322100   PMID:15380020   PMID:15465911   PMID:15466467  
PMID:15489334   PMID:15502874   PMID:15510220   PMID:15579163   PMID:15641770   PMID:15691713   PMID:15863497   PMID:15938614   PMID:16020543   PMID:16030137   PMID:16077187   PMID:16174552  
PMID:16176937   PMID:16227205   PMID:16260631   PMID:16269331   PMID:16298531   PMID:16306404   PMID:16330551   PMID:16423428   PMID:16460685   PMID:16503161   PMID:16600504   PMID:16636270  
PMID:16687662   PMID:16734431   PMID:16764865   PMID:16882008   PMID:16959795   PMID:17029600   PMID:17035541   PMID:17077307   PMID:17085784   PMID:17156375   PMID:17222866   PMID:17250686  
PMID:17273802   PMID:17318638   PMID:17380380   PMID:17408955   PMID:17475220   PMID:17592526   PMID:17610578   PMID:17645694   PMID:17676786   PMID:17689254   PMID:17714497   PMID:17868672  
PMID:17873367   PMID:18065497   PMID:18195004   PMID:18331289   PMID:18333965   PMID:18346205   PMID:18427558   PMID:18449945   PMID:18550842   PMID:18566453   PMID:18614564   PMID:18704197  
PMID:18761401   PMID:18790059   PMID:18804502   PMID:18817762   PMID:18975920   PMID:18980610   PMID:19046408   PMID:19112474   PMID:19146388   PMID:19157893   PMID:19203998   PMID:19224863  
PMID:19493164   PMID:19549071   PMID:19664623   PMID:19692427   PMID:19745811   PMID:19813144   PMID:19875982   PMID:20026244   PMID:20039155   PMID:20071342   PMID:20081243   PMID:20098715  
PMID:20203178   PMID:20345648   PMID:20405200   PMID:20457918   PMID:20511551   PMID:20617407   PMID:20664530   PMID:20697033   PMID:20798282   PMID:20959456   PMID:20974939   PMID:21050448  
PMID:21127069   PMID:21252228   PMID:21272005   PMID:21319811   PMID:21320589   PMID:21325059   PMID:21330369   PMID:21338582   PMID:21443877   PMID:21832049   PMID:21841800   PMID:22065755  
PMID:22119730   PMID:22251432   PMID:22315227   PMID:22619171   PMID:22639889   PMID:22737239   PMID:22833673   PMID:22854022   PMID:22871113   PMID:23077527   PMID:23128054   PMID:23278133  
PMID:23291291   PMID:23431141   PMID:23441091   PMID:23454680   PMID:23507046   PMID:23567316   PMID:23567651   PMID:23610405   PMID:23629650   PMID:23809578   PMID:23927048   PMID:23954626  
PMID:23983262   PMID:24076025   PMID:24178442   PMID:24248062   PMID:24374342   PMID:24664141   PMID:24698767   PMID:24722055   PMID:24747612   PMID:24833599   PMID:24895406   PMID:24927544  
PMID:24936070   PMID:24983211   PMID:25009269   PMID:25019582   PMID:25043722   PMID:25090657   PMID:25195598   PMID:25246573   PMID:25251017   PMID:25446002   PMID:25484190   PMID:25495902  
PMID:25533483   PMID:25561023   PMID:25643172   PMID:25669123   PMID:25732184   PMID:25756858   PMID:25896939   PMID:26075822   PMID:26076669   PMID:26078453   PMID:26158517   PMID:26192120  
PMID:26203154   PMID:26212128   PMID:26378614   PMID:26434717   PMID:26822976   PMID:26907683   PMID:26989132   PMID:27018801   PMID:27133445   PMID:27280685   PMID:27334109   PMID:27477055  
PMID:27581683   PMID:27597756   PMID:27640673   PMID:27708338   PMID:28052246   PMID:28193887   PMID:28288128   PMID:28900007   PMID:28933786   PMID:28984618   PMID:29180624   PMID:29198021  
PMID:29229832   PMID:29337114   PMID:29459792   PMID:29702063   PMID:29749529   PMID:29996045   PMID:30081046   PMID:30132200   PMID:30404828   PMID:30901378   PMID:31034892   PMID:31270237  
PMID:31695184   PMID:32059750   PMID:32113849   PMID:32385113  


Genomics

Candidate Gene Status
Snca is a candidate Gene for QTL Alc18
Snca is a candidate Gene for QTL Alc22
Comparative Map Data
Snca
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2489,696,420 - 89,797,240 (-)NCBI
Rnor_6.0 Ensembl490,782,374 - 90,882,285 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0490,782,412 - 90,883,236 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04155,592,411 - 155,690,724 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4489,613,731 - 89,722,807 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1489,858,155 - 89,967,232 (-)NCBI
Celera484,478,545 - 84,578,894 (-)NCBICelera
Cytogenetic Map4q24NCBI
SNCA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl489,700,345 - 89,838,315 (-)EnsemblGRCh38hg38GRCh38
GRCh38489,724,099 - 89,838,324 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37490,645,250 - 90,759,455 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36490,865,728 - 90,977,156 (-)NCBINCBI36hg18NCBI36
Build 34491,004,212 - 91,114,009NCBI
Celera487,942,196 - 88,056,576 (-)NCBI
Cytogenetic Map4q22.1NCBI
HuRef486,396,384 - 86,510,518 (-)NCBIHuRef
CHM1_1490,621,712 - 90,735,909 (-)NCBICHM1_1
Snca
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39660,708,557 - 60,806,839 (-)NCBIGRCm39mm39
GRCm39 Ensembl660,708,559 - 60,806,839 (-)Ensembl
GRCm38660,731,573 - 60,829,855 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl660,731,575 - 60,829,855 (-)EnsemblGRCm38mm10GRCm38
MGSCv37660,681,567 - 60,779,849 (-)NCBIGRCm37mm9NCBIm37
MGSCv36660,661,161 - 60,759,433 (-)NCBImm8
Celera662,883,898 - 62,982,187 (-)NCBICelera
Cytogenetic Map6B3NCBI
cM Map629.15NCBI
Snca
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955405853,946 - 965,403 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955405854,011 - 962,741 (-)NCBIChiLan1.0ChiLan1.0
SNCA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1492,737,608 - 92,851,720 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl492,737,608 - 92,850,600 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0482,018,585 - 82,132,938 (-)NCBIMhudiblu_PPA_v0panPan3
SNCA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13212,915,871 - 13,079,338 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3212,916,215 - 13,060,383 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3228,876,711 - 29,040,565 (+)NCBI
ROS_Cfam_1.03212,968,680 - 13,133,813 (-)NCBI
UMICH_Zoey_3.13213,053,952 - 13,218,226 (-)NCBI
UNSW_CanFamBas_1.03212,876,233 - 13,041,037 (-)NCBI
UU_Cfam_GSD_1.03226,872,693 - 27,039,258 (+)NCBI
Snca
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530128,380,373 - 28,478,711 (+)NCBI
SpeTri2.0NW_0049366852,077,017 - 2,175,298 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNCA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8129,248,819 - 129,388,307 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18129,247,724 - 129,388,307 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28138,635,406 - 138,774,240 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SNCA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1738,083,154 - 38,194,068 (-)NCBI
ChlSab1.1 Ensembl738,081,509 - 38,191,479 (-)Ensembl
Vero_WHO_p1.0NW_02366603716,869,729 - 16,980,841 (-)NCBI
Snca
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475717,393,046 - 17,528,783 (-)NCBI

Position Markers
Snca  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2489,778,541 - 89,778,671 (+)MAPPER
Rnor_6.0490,864,709 - 90,864,838NCBIRnor6.0
Rnor_5.04155,672,871 - 155,673,000UniSTSRnor5.0
RGSC_v3.4489,705,087 - 89,705,216UniSTSRGSC3.4
Celera484,561,162 - 84,561,291UniSTS
Cytogenetic Map4q24UniSTS
PMC153617P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2489,696,985 - 89,697,976 (+)MAPPER
Rnor_6.0490,782,978 - 90,783,975NCBIRnor6.0
Rnor_5.04155,592,977 - 155,593,974UniSTSRnor5.0
RGSC_v3.4489,614,297 - 89,615,290UniSTSRGSC3.4
Celera484,479,111 - 84,480,101UniSTS
Cytogenetic Map4q24UniSTS
UniSTS:234029  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2489,696,738 - 89,697,005 (+)MAPPER
Rnor_6.0490,782,731 - 90,782,997NCBIRnor6.0
Rnor_5.04155,592,730 - 155,592,996UniSTSRnor5.0
RGSC_v3.4489,614,050 - 89,614,316UniSTSRGSC3.4
Celera484,478,864 - 84,479,130UniSTS
Cytogenetic Map4q24UniSTS
PMC153617P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2489,696,461 - 89,696,566 (+)MAPPER
Rnor_6.0490,782,454 - 90,782,558NCBIRnor6.0
Rnor_5.04155,592,453 - 155,592,557UniSTSRnor5.0
RGSC_v3.4489,613,773 - 89,613,877UniSTSRGSC3.4
Celera484,478,587 - 84,478,691UniSTS
Cytogenetic Map4q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)43043231145254791Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)4734240492484039Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)429549895112807890Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)43427793299067150Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)436615599145611886Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)437703272115372927Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)443414605155469929Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)443414792146942075Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)443414792146942075Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)446898276145611886Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)449906054145611886Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)455324953148360954Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)455375865125671711Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45579156492484312Rat
1578657Bss12Bone structure and strength QTL 128.9femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)456092756101092756Rat
1578658Bss13Bone structure and strength QTL 138femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)456092756101092756Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)45710107792990863Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)458166424103166424Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)458640017154427984Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
1549843Bw53Body weight QTL 530.0001body mass (VT:0001259)body weight gain (CMO:0000420)46043912799066957Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)460439127113416139Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)461038901127777403Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in pulse pressure (CMO:0001882)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in systolic blood pressure (CMO:0000747)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in mean arterial blood pressure (CMO:0002035)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)461708341113100992Rat
2300179Bmd50Bone mineral density QTL 505.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)461975371106975371Rat
1641919Alc22Alcohol consumption QTL 220.0005drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)462947687125671711Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)463537179157286626Rat
6478684Anxrr30Anxiety related response QTL 300.00087defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)463812687108812687Rat
6478743Anxrr40Anxiety related response QTL 400.83076defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)463812687108812687Rat
6478772Anxrr49Anxiety related response QTL 490.15488defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)463812687108812687Rat
631651Bp124Blood pressure QTL 1243arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)463938412108938412Rat
2312569Pur19Proteinuria QTL 193.40.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)46598924397759057Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)470773471132455556Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)471476518116476518Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)471476518116476518Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)473786419132455556Rat
724522Bp146Blood pressure QTL 1462.20.0021arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)475258970120258970Rat
2302051Pia28Pristane induced arthritis QTL 285.30.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)475258970120258970Rat
738015Pia9Pristane induced arthritis QTL 94.50.048joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)476567036121567036Rat
70167Bw22Body weight QTL 223.1body mass (VT:0001259)body weight (CMO:0000012)477307388116916073Rat
1357342Bw40Body weight QTL 400.001body mass (VT:0001259)body weight (CMO:0000012)477307388116916073Rat
631662Hcar2Hepatocarcinoma resistance QTL 23.10.0003liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)479555067124555067Rat
631556Bp135Blood pressure QTL 1350.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)479557856116916073Rat
61364Iddm2Insulin dependent diabetes mellitus QTL 2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47956245198542106Rat
2306899Bp338Blood pressure QTL 3380.071arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)481874073119546974Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)481959983152055009Rat
2306794Ean2Experimental allergic neuritis QTL 26.4nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)48447525797479149Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)484475257178931073Rat
634334Xhs3X-ray hypersensitivity QTL 310intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)485794049129615056Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)486312589146942261Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)486312589147702403Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486438317168047091Rat
61476Aia3Adjuvant induced arthritis QTL 33.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)486532519131532519Rat
1578662Bss15Bone structure and strength QTL 1519.6femur width (VT:1000666)femoral neck width (CMO:0001695)487136446132136446Rat
1578670Bss14Bone structure and strength QTL 1416.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)487136446132136446Rat
2317587Eae26Experimental allergic encephalomyelitis QTL 26nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)48977755299067150Rat


Related Rat Strains
The following Strains have been annotated to Snca

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:164
Count of miRNA genes:128
Interacting mature miRNAs:144
Transcripts:ENSRNOT00000039247, ENSRNOT00000042485
Prediction methods:Microtar, 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 16 18 18 11 18 66 2 7 2
Low 3 27 31 15 8 15 8 9 8 32 30 9 8
Below cutoff 8 8 8 2 1 4

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_019169 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236591 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF007758 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY550005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY550006 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC087682 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474042 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ163910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ163911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212580 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227096 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000142 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MG016712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S73007 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S73008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000039247   ⟹   ENSRNOP00000030609
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl490,782,374 - 90,882,285 (-)Ensembl
RefSeq Acc Id: NM_019169   ⟹   NP_062042
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2489,696,420 - 89,796,262 (-)NCBI
Rnor_6.0490,782,412 - 90,882,258 (-)NCBI
Rnor_5.04155,592,411 - 155,690,724 (-)NCBI
RGSC_v3.4489,613,731 - 89,722,807 (-)RGD
Celera484,478,545 - 84,578,894 (-)RGD
Sequence:
RefSeq Acc Id: XM_006236591   ⟹   XP_006236653
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2489,717,071 - 89,796,554 (-)NCBI
Rnor_6.0490,803,196 - 90,882,613 (-)NCBI
Rnor_5.04155,592,411 - 155,690,724 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592500   ⟹   XP_017447989
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2489,717,071 - 89,797,240 (-)NCBI
Rnor_6.0490,803,196 - 90,883,236 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039107198   ⟹   XP_038963126
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2489,736,620 - 89,796,524 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_062042   ⟸   NM_019169
- UniProtKB: P37377 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006236653   ⟸   XM_006236591
- Peptide Label: isoform X1
- UniProtKB: P37377 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017447989   ⟸   XM_017592500
- Peptide Label: isoform X1
- UniProtKB: P37377 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000030609   ⟸   ENSRNOT00000039247
RefSeq Acc Id: XP_038963126   ⟸   XM_039107198
- Peptide Label: isoform X2

Transcriptome

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

Promoters
RGD ID:13693091
Promoter ID:EPDNEW_R3616
Type:multiple initiation site
Name:Snca_1
Description:synuclein alpha
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_6.0490,882,250 - 90,882,310EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3729 AgrOrtholog
Ensembl Genes ENSRNOG00000008656 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000030609 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000039247 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7321273 IMAGE-MGC_LOAD
InterPro Synuclein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synuclein_alpha UniProtKB/Swiss-Prot
KEGG Report rno:29219 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105443 IMAGE-MGC_LOAD
NCBI Gene 29219 ENTREZGENE
PANTHER PTHR13820 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR13820:SF5 UniProtKB/Swiss-Prot
Pfam Synuclein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Snca PhenoGen
PRINTS ASYNUCLEIN UniProtKB/Swiss-Prot
  SYNUCLEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC217930
UniProt P37377 ENTREZGENE
  Q3LVE5_RAT UniProtKB/TrEMBL
  SYUA_RAT UniProtKB/Swiss-Prot
UniProt Secondary P37378 UniProtKB/Swiss-Prot
  Q53YM9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-20 Snca  synuclein alpha  Snca  synuclein, alpha (non A4 component of amyloid precursor)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-18 Snca  synuclein, alpha (non A4 component of amyloid precursor)  Snca  synuclein, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Snca  synuclein, alpha      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease may play a role in several neurodegenerative disorders, including dementia with Lewy bodies, multiple system atrophy, and Parkinson's disease 631849
gene_disease mutations of the human homolog are detected in some families with an autosomal dominant form of Parkinson's Disease 730239
gene_expression expressed in central nervous system, and enriched in presynaptic nerve terminals 631849
gene_expression mRNA and protein levels in the hippocampus and caudate putamen were higher in inbred alcohol preferring (P) than alcohol non-preferring (NP) rats 631849
gene_expression expression in neurons of substantia nigra is upregulated during postnatal development 730046
gene_process reduces dopamine synthesis by inhibition of the activity of tyrosine hydroxylase 631849
gene_protein 140 amino acids 70015
gene_protein 140 amino acids 631849
gene_regulation a nucleotide exchange in the 3' UTR reduced expression of the luciferase reporter gene in SK-N-SH neuroblastoma cells 631849