Sncb (synuclein, beta) - Rat Genome Database

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Gene: Sncb (synuclein, beta) Rattus norvegicus
Analyze
Symbol: Sncb
Name: synuclein, beta
RGD ID: 70992
Description: Enables alpha-tubulin binding activity and beta-tubulin binding activity. Predicted to be involved in several processes, including chemical synaptic transmission; regulation of neuron death; and synaptic vesicle endocytosis. Predicted to act upstream of or within dopamine metabolic process and negative regulation of neuron apoptotic process. Located in growth cone; neuronal cell body; and terminal bouton. Is active in presynaptic cytosol. Used to study uveitis. Human ortholog(s) of this gene implicated in Lewy body dementia and Parkinson's disease. Orthologous to human SNCB (synuclein beta); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: beta-synuclein; phosphoneuroprotein 14; PNP 14
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
mRatBN7.2179,846,802 - 9,855,013 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl179,846,802 - 9,855,012 (+)Ensembl
Rnor_6.01710,384,472 - 10,392,776 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1710,384,511 - 10,392,843 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01712,510,521 - 12,518,728 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41715,907,498 - 15,915,705 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11715,907,640 - 15,915,194 (+)NCBI
Celera179,921,982 - 9,930,166 (+)NCBICelera
Cytogenetic Map17p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Beta-synuclein gene variants and Parkinson's disease: a preliminary case-control study. Brighina L, etal., Neurosci Lett. 2007 Jun 15;420(3):229-34. Epub 2007 May 21.
2. Neurodegeneration with brain iron accumulation, type 1 is characterized by alpha-, beta-, and gamma-synuclein neuropathology. Galvin JE, etal., Am J Pathol. 2000 Aug;157(2):361-8.
3. Axon pathology in Parkinson's disease and Lewy body dementia hippocampus contains alpha-, beta-, and gamma-synuclein. Galvin JE, etal., Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13450-5.
4. 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.
5. Prominent perikaryal expression of alpha- and beta-synuclein in neurons of dorsal root ganglion and in medullary neurons. Giasson BI, etal., Exp Neurol. 2001 Dec;172(2):354-62.
6. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
7. An antiaggregation gene therapy strategy for Lewy body disease utilizing beta-synuclein lentivirus in a transgenic model. Hashimoto M, etal., Gene Ther. 2004 Dec;11(23):1713-23.
8. Desipramine modulation of alpha-, gamma-synuclein, and the norepinephrine transporter in an animal model of depression. Jeannotte AM, etal., Neuropsychopharmacology. 2009 Mar;34(4):987-98. Epub 2008 Sep 17.
9. Differential localization of alpha-, beta- and gamma-synucleins in the rat CNS. Li JY, etal., Neuroscience. 2002;113(2):463-78.
10. Alpha- and beta-synucleins are new diagnostic tools for acute erythroid leukemia and acute megakaryoblastic leukemia. Maitta RW, etal., Am J Hematol. 2011 Feb;86(2):230-4. doi: 10.1002/ajh.21932.
11. Gene Data Set MGD Curation, June 12, 2002
12. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
13. Autoimmune encephalomyelitis and uveitis induced by T cell immunity to self beta-synuclein. Mor F, etal., J Immunol 2003 Jan 1;170(1):628-34.
14. Pick's disease: alpha- and beta-synuclein-immunoreactive Pick bodies in the dentate gyrus. Mori F, etal., Acta Neuropathol. 2002 Nov;104(5):455-61. Epub 2002 Jul 2.
15. Synucleins are developmentally expressed, and alpha-synuclein regulates the size of the presynaptic vesicular pool in primary hippocampal neurons. Murphy DD, etal., J Neurosci 2000 May 1;20(9):3214-20.
16. Localization of phosphoneuroprotein 14 (PNP 14) and its mRNA expression in rat brain determined by immunocytochemistry and in situ hybridization. Nakajo S, etal., Brain Res Mol Brain Res. 1994 Nov;27(1):81-6.
17. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Beta-synuclein gene alterations in dementia with Lewy bodies. Ohtake H, etal., Neurology. 2004 Sep 14;63(5):805-11.
19. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
20. Localization of alpha-, beta-, and gamma-synuclein during neuronal development and alterations associated with the neuronal response to axonal trauma. Quilty MC, etal., Exp Neurol 2003 Jul;182(1):195-207.
21. GOA pipeline RGD automated data pipeline
22. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
23. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
24. Altered expression of the synuclein family mRNA in Lewy body and Alzheimer's disease. Rockenstein E, etal., Brain Res. 2001 Sep 28;914(1-2):48-56.
25. Neuronal accumulation of alpha- and beta-synucleins in the brain of a GM2 gangliosidosis mouse model. Suzuki K, etal., Neuroreport. 2003 Mar 24;14(4):551-4.
26. Cloning and characterization of the cDNA encoding a novel brain-specific 14-kDa protein. Tobe T, etal., J Neurochem 1992 Nov;59(5):1624-9.
27. Age-dependent synuclein pathology following traumatic brain injury in mice. Uryu K, etal., Exp Neurol. 2003 Nov;184(1):214-24.
28. Composition of isolated synaptic boutons reveals the amounts of vesicle trafficking proteins. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
Additional References at PubMed
PMID:8223629   PMID:10964942   PMID:11312271   PMID:12477932   PMID:14651853   PMID:15465911   PMID:15489334   PMID:16269331   PMID:16483693   PMID:17085784   PMID:17222866   PMID:19692427  
PMID:20974939   PMID:21699177   PMID:22871113   PMID:25002582   PMID:25009269   PMID:25495902   PMID:29808713   PMID:30787438   PMID:33428933  


Genomics

Comparative Map Data
Sncb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2179,846,802 - 9,855,013 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl179,846,802 - 9,855,012 (+)Ensembl
Rnor_6.01710,384,472 - 10,392,776 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1710,384,511 - 10,392,843 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01712,510,521 - 12,518,728 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41715,907,498 - 15,915,705 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11715,907,640 - 15,915,194 (+)NCBI
Celera179,921,982 - 9,930,166 (+)NCBICelera
Cytogenetic Map17p14NCBI
SNCB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385176,620,082 - 176,630,534 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl5176,620,082 - 176,630,556 (-)EnsemblGRCh38hg38GRCh38
GRCh375176,047,083 - 176,057,535 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365175,979,816 - 175,990,163 (-)NCBINCBI36hg18NCBI36
Build 345175,979,816 - 175,990,163NCBI
Celera5172,442,697 - 172,464,864 (+)NCBI
Cytogenetic Map5q35.2NCBI
HuRef5170,970,990 - 170,981,256 (-)NCBIHuRef
CHM1_15175,479,633 - 175,489,981 (-)NCBICHM1_1
T2T-CHM13v2.05177,166,665 - 177,177,114 (-)NCBI
Sncb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391354,906,673 - 54,914,435 (-)NCBIGRCm39mm39
GRCm39 Ensembl1354,906,673 - 54,914,408 (-)Ensembl
GRCm381354,758,860 - 54,766,622 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1354,758,860 - 54,766,595 (-)EnsemblGRCm38mm10GRCm38
MGSCv371354,860,221 - 54,867,801 (-)NCBIGRCm37mm9NCBIm37
MGSCv361354,768,482 - 54,776,062 (-)NCBImm8
Celera1355,824,326 - 55,831,944 (-)NCBICelera
Cytogenetic Map13B1NCBI
cM Map1329.28NCBI
Sncb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540828,894,204 - 28,903,095 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540828,894,204 - 28,903,095 (-)NCBIChiLan1.0ChiLan1.0
SNCB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15178,988,314 - 178,998,805 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5178,988,439 - 178,998,800 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05171,918,297 - 171,928,672 (-)NCBIMhudiblu_PPA_v0panPan3
SNCB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1436,710,236 - 36,719,455 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl436,616,039 - 36,764,501 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha436,677,103 - 36,686,289 (+)NCBI
ROS_Cfam_1.0437,076,409 - 37,085,600 (+)NCBI
ROS_Cfam_1.0 Ensembl437,048,276 - 37,103,097 (+)Ensembl
UMICH_Zoey_3.1436,902,261 - 36,911,447 (+)NCBI
UNSW_CanFamBas_1.0437,089,947 - 37,099,120 (+)NCBI
UU_Cfam_GSD_1.0437,598,214 - 37,607,385 (+)NCBI
Sncb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213121,853,363 - 121,863,441 (-)NCBI
SpeTri2.0NW_004936597878,270 - 888,346 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNCB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl281,287,878 - 81,302,863 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1281,287,764 - 81,302,859 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2282,889,540 - 82,899,597 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SNCB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12378,626,876 - 78,637,337 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2378,627,479 - 78,636,287 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660759,760,600 - 9,770,954 (-)NCBIVero_WHO_p1.0
Sncb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473313,506,180 - 13,513,712 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462473313,506,181 - 13,513,979 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
Sncb  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2179,846,751 - 9,846,962 (+)MAPPERmRatBN7.2
Rnor_6.01710,384,519 - 10,384,729NCBIRnor6.0
Rnor_5.01712,510,471 - 12,510,681UniSTSRnor5.0
RGSC_v3.41715,907,448 - 15,907,658UniSTSRGSC3.4
Celera179,921,932 - 9,922,142UniSTS
Cytogenetic Map17p14UniSTS
AI145381  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2179,854,698 - 9,854,918 (+)MAPPERmRatBN7.2
Rnor_6.01710,392,462 - 10,392,681NCBIRnor6.0
Rnor_5.01712,518,414 - 12,518,633UniSTSRnor5.0
RGSC_v3.41715,915,391 - 15,915,610UniSTSRGSC3.4
Celera179,929,852 - 9,930,071UniSTS
RH 3.4 Map1794.3UniSTS
Cytogenetic Map17p14UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)17429913021293263Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17429913021293263Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
1581553Pur14Proteinuria QTL 145.30.0001total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17797996816317111Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17920136523653323Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17920136523653323Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17920136523653323Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:333
Count of miRNA genes:185
Interacting mature miRNAs:219
Transcripts:ENSRNOT00000024357
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 2 62 13
Low 3 20 1 1 1 12 20 1
Below cutoff 14 22 11 5 11 5 5 6 8 8 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024357   ⟹   ENSRNOP00000024357
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl179,846,802 - 9,855,012 (+)Ensembl
Rnor_6.0 Ensembl1710,384,511 - 10,392,843 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108686   ⟹   ENSRNOP00000096826
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl179,847,041 - 9,855,012 (+)Ensembl
RefSeq Acc Id: NM_080777   ⟹   NP_542955
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,846,802 - 9,855,013 (+)NCBI
Rnor_6.01710,384,569 - 10,392,776 (+)NCBI
Rnor_5.01712,510,521 - 12,518,728 (+)NCBI
RGSC_v3.41715,907,498 - 15,915,705 (+)RGD
Celera179,921,982 - 9,930,166 (+)RGD
Sequence:
RefSeq Acc Id: XM_006253594   ⟹   XP_006253656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,847,279 - 9,855,013 (+)NCBI
Rnor_6.01710,384,472 - 10,392,776 (+)NCBI
Rnor_5.01712,510,521 - 12,518,728 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_542955   ⟸   NM_080777
- UniProtKB: Q63754 (UniProtKB/Swiss-Prot),   A0A0G2JSQ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253656   ⟸   XM_006253594
- Peptide Label: isoform X1
- UniProtKB: Q63754 (UniProtKB/Swiss-Prot),   A0A0G2JSQ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024357   ⟸   ENSRNOT00000024357
RefSeq Acc Id: ENSRNOP00000096826   ⟸   ENSRNOT00000108686

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63754-F1-model_v2 AlphaFold Q63754 1-137 view protein structure

Transcriptome

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

Promoters
RGD ID:13700317
Promoter ID:EPDNEW_R10841
Type:multiple initiation site
Name:Sncb_1
Description:synuclein, beta
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_6.01710,384,500 - 10,384,560EPDNEW

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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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:70992 AgrOrtholog
BioCyc Gene G2FUF-10181 BioCyc
Ensembl Genes ENSRNOG00000018039 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024357 ENTREZGENE
  ENSRNOP00000024357.6 UniProtKB/TrEMBL
  ENSRNOP00000096826.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024357 ENTREZGENE
  ENSRNOT00000024357.7 UniProtKB/TrEMBL
  ENSRNOT00000108686.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7314241 IMAGE-MGC_LOAD
InterPro Synuclein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synuclein_beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:113893 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:105340 IMAGE-MGC_LOAD
NCBI Gene 113893 ENTREZGENE
PANTHER PTHR13820 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR13820:SF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Synuclein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sncb PhenoGen
PRINTS BSYNUCLEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYNUCLEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JSQ1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6ATA5_RAT UniProtKB/TrEMBL
  Q63754 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q5PPN9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-07-09 Sncb  synuclein, beta      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization found in the cellular cytosol and at the growth cones of developing axons early in development, but later distribution becomes punctate within axons and growth cones; after axonal injury, accumulates in the damaged axons, localizing to cytoskeletal abnormalities 1358136
gene_cellular_localization cortical neurons express both alpha- and beta-synuclein but distribution of the isoforms is nonoverlapping within individual neurons 1358136
gene_disease autoimmunity to sncb leads to encephalomyelitis 730073
gene_expression mRNA expressed specifically in brain 70615
gene_expression protein found in heavy myelin as well as neurons 730073
gene_protein 137 aa sequence codes for an acidic 14 kDa protein 70615