Syp (synaptophysin) - Rat Genome Database

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Gene: Syp (synaptophysin) Rattus norvegicus
Analyze
Symbol: Syp
Name: synaptophysin
RGD ID: 3802
Description: Exhibits protein domain specific binding activity and syntaxin-1 binding activity. Involved in endocytosis; regulation of opioid receptor signaling pathway; and response to amyloid-beta. Localizes to several cellular components, including excitatory synapse; integral component of synaptic vesicle membrane; and postsynaptic density. Biomarker of Alzheimer's disease. Human ortholog(s) of this gene implicated in non-syndromic X-linked intellectual disability 96. Orthologous to human SYP (synaptophysin); INTERACTS WITH (+)-pilocarpine; (S)-amphetamine; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: major synaptic vesicle protein p38; Syp1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,849,444 - 14,864,553 (-)NCBI
Rnor_6.0 EnsemblX15,695,566 - 15,707,436 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X15,694,699 - 15,709,244 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X16,485,963 - 16,501,050 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,890,307 - 26,905,319 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,943,775 - 26,958,788 (-)NCBI
CeleraX14,932,808 - 14,947,852 (-)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(S)-amphetamine  (EXP)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,2,2-tetramine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-(1,4-diazepane-1-sulfonyl)isoquinoline  (EXP)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (ISO)
abacavir  (ISO)
acetic acid  (ISO)
acrylamide  (EXP)
agomelatine  (EXP)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (ISO)
aluminium sulfate (anhydrous)  (ISO)
ammonium chloride  (EXP)
Aroclor 1254  (EXP)
atorvastatin calcium  (EXP)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bromochloroacetic acid  (ISO)
Butylparaben  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
carbamazepine  (ISO)
carbon nanotube  (EXP)
carmustine  (EXP)
CHIR 99021  (ISO)
chlorohydrocarbon  (ISO)
chloroquine  (EXP)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (EXP,ISO)
citric acid  (EXP)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (ISO)
D-glucose  (EXP)
DDE  (EXP)
decabromodiphenyl ether  (EXP,ISO)
dexamethasone  (EXP)
dibutyl phthalate  (EXP)
dichlorine  (EXP)
enzacamene  (EXP)
epoxiconazole  (EXP)
ethanol  (EXP,ISO)
fasudil hydrochloride  (EXP)
finasteride  (EXP)
fluoxetine  (EXP,ISO)
flutamide  (EXP)
folic acid  (ISO)
fonofos  (ISO)
gamma-tocopherol  (ISO)
glucose  (EXP)
hydralazine  (ISO)
hydrogen peroxide  (ISO)
L-methionine  (ISO)
lactacystin  (EXP)
lead diacetate  (EXP,ISO)
lead tetraacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
linuron  (EXP)
lipopolysaccharide  (ISO)
melatonin  (EXP)
methamphetamine  (EXP,ISO)
methylmercury chloride  (ISO)
Mipafox  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (EXP)
N-ethyl-N-nitrosourea  (EXP)
N-methyl-N-nitrosourea  (EXP)
naphthalene  (ISO)
nicotinic acid  (EXP)
ozone  (EXP)
paracetamol  (ISO)
paraoxon  (ISO)
paraquat  (EXP)
parathion  (ISO)
PCB138  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
permethrin  (ISO)
phenytoin  (ISO)
physostigmine  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
Pyridostigmine bromide  (ISO)
pyrrolidine dithiocarbamate  (ISO)
resveratrol  (ISO)
scopolamine  (EXP)
silver atom  (EXP)
silver(0)  (EXP)
sodium fluoride  (EXP,ISO)
streptozocin  (EXP,ISO)
styrene oxide  (ISO)
sulfur dioxide  (EXP)
sulindac  (EXP)
tadalafil  (ISO)
telmisartan  (EXP,ISO)
terbufos  (ISO)
thioacetamide  (ISO)
thyroxine  (ISO)
tocopherol  (ISO)
trichlorfon  (ISO)
trichostatin A  (EXP)
trimellitic anhydride  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
valsartan  (EXP,ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)
WIN 55212-2  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
1. Antonin W, etal., J Neurosci 2000 Aug 1;20(15):5724-32.
2. Bargou RC and Leube RE, Gene 1991 Mar 15;99(2):197-204.
3. Belfort GM and Kandror KV, J Biol Chem. 2003 Nov 28;278(48):47971-8. Epub 2003 Aug 18.
4. Cao Y, etal., J Alzheimers Dis. 2010;22(1):329-42. doi: 10.3233/JAD-2010-100162.
5. Fenster SD, etal., Neuron 2000 Jan;25(1):203-14.
6. Galli T, etal., J Biol Chem. 1996 Jan 26;271(4):2193-8.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. Ishibashi H Cell Mol Neurobiol 2002 Apr;22(2):191-5.
10. Ito H, etal., J Neurochem. 2008 Oct;107(1):61-72. doi: 10.1111/j.1471-4159.2008.05585.x. Epub 2008 Jul 24.
11. Ito H, etal., J Neurochem. 2009 Feb;108(4):867-80. doi: 10.1111/j.1471-4159.2008.05849.x.
12. Jahn R, etal., Proc Natl Acad Sci U S A. 1985 Jun;82(12):4137-41.
13. Jang S, etal., Nat Neurosci. 2016 Jan;19(1):84-93. doi: 10.1038/nn.4176. Epub 2015 Nov 23.
14. Ko J, etal., EMBO J. 2009 Oct 21;28(20):3244-55. doi: 10.1038/emboj.2009.249. Epub 2009 Sep 3.
15. Leube RE, etal., EMBO J 1987 Nov;6(11):3261-8.
16. Li H, etal., Nat Cell Biol. 2013 Jul;15(7):773-85. doi: 10.1038/ncb2791. Epub 2013 Jun 23.
17. Li S, etal., Neuroscience 2002;115(4):1221-9.
18. Liang YJ, etal., Mol Pharmacol. 2007 Jan;71(1):123-31. Epub 2006 Sep 27.
19. Maienschein V, etal., Glia. 1999 May;26(3):233-44.
20. Martins F, etal., Sci Rep. 2018 Feb 23;8(1):3548. doi: 10.1038/s41598-018-21453-3.
21. McMahon HT, etal., Cell 1995 Oct 6;83(1):111-9.
22. MGD data from the GO Consortium
23. Misra C, etal., Mol Cell Neurosci. 2010 Apr;43(4):341-52. Epub 2010 Jan 18.
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. OMIM Disease Annotation Pipeline
26. Pennuto M, etal., Mol Biol Cell. 2002 Aug;13(8):2706-17.
27. RGD automated data pipeline
28. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
29. RGD automated import pipeline for gene-chemical interactions
30. Rizzoli SO, etal., Traffic. 2006 Sep;7(9):1163-76.
31. Segura I, etal., Nat Neurosci. 2007 Mar;10(3):301-10. Epub 2007 Feb 18.
32. Sudhof TC, etal., Nucleic Acids Res 1987 Nov 25;15(22):9607.
33. Wheeler TC, etal., J Biol Chem 2002 Mar 22;277(12):10273-82.
34. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
Additional References at PubMed
PMID:3120313   PMID:3121632   PMID:8838578   PMID:9364068   PMID:10595519   PMID:10620806   PMID:10712642   PMID:10825299   PMID:10995443   PMID:11879655   PMID:11956199   PMID:12074840  
PMID:12115694   PMID:12202822   PMID:12368914   PMID:12477932   PMID:12498786   PMID:12533614   PMID:12805290   PMID:12965244   PMID:14622577   PMID:15071120   PMID:15328414   PMID:15584914  
PMID:15748150   PMID:15789763   PMID:15964096   PMID:16174552   PMID:16407767   PMID:16980967   PMID:16987241   PMID:16990974   PMID:17018287   PMID:17046993   PMID:17141532   PMID:17330749  
PMID:17360631   PMID:17823315   PMID:17970739   PMID:18279309   PMID:18497889   PMID:18626794   PMID:18692536   PMID:18703118   PMID:18706977   PMID:19019428   PMID:19253017   PMID:19506089  
PMID:19603498   PMID:20025630   PMID:20035832   PMID:20203623   PMID:20422983   PMID:20646586   PMID:20826656   PMID:21307259   PMID:21556117   PMID:21658579   PMID:21664258   PMID:21687946  
PMID:21884692   PMID:22905234   PMID:22970294   PMID:23103755   PMID:23704327   PMID:23986251   PMID:24861887   PMID:25282817   PMID:25697061   PMID:26316168   PMID:26682524   PMID:26794272  
PMID:26854222   PMID:27389246   PMID:28372486   PMID:28801169   PMID:29350434   PMID:29490264   PMID:29545098   PMID:30911273   PMID:31146894  


Genomics

Comparative Map Data
Syp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,849,444 - 14,864,553 (-)NCBI
Rnor_6.0 EnsemblX15,695,566 - 15,707,436 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X15,694,699 - 15,709,244 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X16,485,963 - 16,501,050 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,890,307 - 26,905,319 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,943,775 - 26,958,788 (-)NCBI
CeleraX14,932,808 - 14,947,852 (-)NCBICelera
Cytogenetic MapXq12NCBI
SYP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX49,187,804 - 49,200,259 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 EnsemblX49,187,815 - 49,200,199 (-)EnsemblGRCh38hg38GRCh38
GRCh38X49,187,815 - 49,200,193 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X49,044,268 - 49,056,652 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,931,209 - 48,943,605 (-)NCBINCBI36hg18NCBI36
Build 34X48,800,635 - 48,813,032NCBI
CeleraX52,607,708 - 52,620,104 (+)NCBI
Cytogenetic MapXp11.23NCBI
HuRefX46,701,336 - 46,713,608 (-)NCBIHuRef
CHM1_1X49,076,586 - 49,088,982 (-)NCBICHM1_1
Syp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X7,504,819 - 7,519,495 (+)NCBIGRCm39mm39
GRCm39 EnsemblX7,504,710 - 7,519,495 (+)Ensembl
GRCm38X7,638,580 - 7,653,256 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX7,638,471 - 7,653,256 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X7,215,706 - 7,230,382 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X6,795,670 - 6,810,210 (+)NCBImm8
CeleraX3,817,995 - 3,833,335 (-)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.44NCBI
Syp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955543675,294 - 689,686 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955543675,294 - 689,579 (-)NCBIChiLan1.0ChiLan1.0
SYP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X49,340,021 - 49,352,420 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX49,340,021 - 49,352,420 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X41,487,538 - 41,500,039 (-)NCBIMhudiblu_PPA_v0panPan3
SYP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X42,288,071 - 42,301,802 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX42,288,148 - 42,299,487 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX16,666,206 - 16,678,233 (-)NCBI
ROS_Cfam_1.0X42,429,161 - 42,441,205 (-)NCBI
UMICH_Zoey_3.1X42,413,127 - 42,425,154 (-)NCBI
UNSW_CanFamBas_1.0X42,400,777 - 42,412,809 (-)NCBI
UU_Cfam_GSD_1.0X42,495,540 - 42,507,567 (-)NCBI
LOC101975550
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X34,821,818 - 34,835,592 (-)NCBI
SpeTri2.0NW_0049367211,062,206 - 1,075,935 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX43,232,195 - 43,246,682 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X43,232,190 - 43,246,764 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X48,080,132 - 48,094,682 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103231965
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X46,287,610 - 46,299,926 (-)NCBI
ChlSab1.1 EnsemblX46,287,282 - 46,299,773 (-)Ensembl
Syp
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624893929,460 - 942,806 (-)NCBI

Position Markers
DXMgh1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,865,458 - 14,865,602 (+)MAPPER
Rnor_6.0X15,710,150 - 15,710,293NCBIRnor6.0
Rnor_5.0X16,501,617 - 16,501,760UniSTSRnor5.0
RGSC_v3.4X26,906,212 - 26,906,356RGDRGSC3.4
RGSC_v3.4X26,906,213 - 26,906,356UniSTSRGSC3.4
RGSC_v3.1X26,959,681 - 26,959,825RGD
CeleraX14,948,758 - 14,948,901UniSTS
RH 3.4 MapX161.0UniSTS
RH 3.4 MapX161.0RGD
RH 2.0 Map21113.4RGD
Cytogenetic MapXq13-q14UniSTS
DXWox12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,865,545 - 14,865,582 (+)MAPPER
Rnor_6.0X15,710,237 - 15,710,273NCBIRnor6.0
Rnor_5.0X16,501,704 - 16,501,740UniSTSRnor5.0
RGSC_v3.4X26,906,299 - 26,906,336RGDRGSC3.4
RGSC_v3.4X26,906,300 - 26,906,336UniSTSRGSC3.4
RGSC_v3.1X26,959,768 - 26,959,805RGD
CeleraX14,948,845 - 14,948,881UniSTS
RH 3.4 MapX161.0UniSTS
RH 3.4 MapX161.0RGD
RH 2.0 Map21114.7RGD
Cytogenetic MapXq13-q14UniSTS
RH132023  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,849,483 - 14,849,685 (+)MAPPER
Rnor_6.0X15,694,739 - 15,694,940NCBIRnor6.0
Rnor_5.0X16,485,714 - 16,485,915UniSTSRnor5.0
RGSC_v3.4X26,890,343 - 26,890,544UniSTSRGSC3.4
CeleraX14,932,848 - 14,933,049UniSTS
RH 3.4 MapX167.0UniSTS
Cytogenetic MapXq13UniSTS
Cytogenetic MapXq13-q14UniSTS
GDB:216846  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,853,579 - 14,853,917 (+)MAPPER
Rnor_6.0X15,698,834 - 15,699,171NCBIRnor6.0
Rnor_5.0X16,489,809 - 16,490,146UniSTSRnor5.0
RGSC_v3.4X26,894,438 - 26,894,775UniSTSRGSC3.4
CeleraX14,936,944 - 14,937,281UniSTS
Cytogenetic MapXq13-q14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X166245321592783Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X183816624331837Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:603
Count of miRNA genes:273
Interacting mature miRNAs:342
Transcripts:ENSRNOT00000013724
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 7
Medium 6 63 3
Low 3 24 32 22 18 22 4 4 4 35 33 10 4
Below cutoff 19 19 19 1 19 4 7 3 1 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000085907   ⟹   ENSRNOP00000075360
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX15,695,566 - 15,707,436 (-)Ensembl
RefSeq Acc Id: NM_012664   ⟹   NP_036796
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,849,444 - 14,864,553 (-)NCBI
Rnor_6.0X15,694,699 - 15,709,244 (-)NCBI
Rnor_5.0X16,485,963 - 16,501,050 (-)NCBI
RGSC_v3.4X26,890,307 - 26,905,319 (-)RGD
CeleraX14,932,808 - 14,947,852 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036796   ⟸   NM_012664
- UniProtKB: P07825 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075360   ⟸   ENSRNOT00000085907
Protein Domains
MARVEL

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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:3802 AgrOrtholog
Ensembl Genes ENSRNOG00000059720 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000075360 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000085907 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7936715 IMAGE-MGC_LOAD
InterPro Marvel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synaptophysin/porin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24804 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124631 IMAGE-MGC_LOAD
NCBI Gene 24804 ENTREZGENE
PANTHER PTHR10306 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10306:SF10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam MARVEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Syp PhenoGen
PRINTS SYNAPTOPHYSN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE MARVEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYNAPTOP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2KAD8_RAT UniProtKB/TrEMBL
  P07825 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q499R3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Syp  Synaptophysin      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization integral membrane glycoprotein component of synaptic vesicles 730209
gene_expression found in small synaptic vesicles in brain and endocrine cells  
gene_process may be involved in structural functions such as organizing other membrane components or targeting the vesicles to the plasma membrane