Syp (synaptophysin) - Rat Genome Database

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Gene: Syp (synaptophysin) Rattus norvegicus
Symbol: Syp
Name: synaptophysin
RGD ID: 3802
Description: Enables protein domain specific binding activity and syntaxin-1 binding activity. Involved in endocytosis; regulation of opioid receptor signaling pathway; and response to amyloid-beta. Located in several cellular components, including postsynaptic density; presynaptic active zone; and synaptic vesicle. Part of protein-containing complex. Is active in synaptic vesicle membrane. 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
Previously known as: major synaptic vesicle protein p38; Syp1
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.2X14,849,444 - 14,864,553 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX14,849,444 - 14,864,745 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX19,663,795 - 19,678,920 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X20,404,212 - 20,419,339 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0X16,669,360 - 16,684,482 (+)NCBIRnor_WKY
Rnor_6.0X15,694,699 - 15,709,244 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,695,566 - 15,707,436 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X16,485,963 - 16,501,050 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,890,307 - 26,905,319 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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)

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-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)
antimycin A  (ISO)
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)
cannabidiol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (EXP)
carmustine  (EXP)
CGP 52608  (ISO)
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)
decabromodiphenyl ether  (EXP,ISO)
deguelin  (ISO)
dexamethasone  (EXP)
dibutyl phthalate  (EXP)
dichlorine  (EXP)
dihydroactinidiolide  (ISO)
dimethylselenide  (ISO)
donepezil hydrochloride  (ISO)
enzacamene  (EXP)
epoxiconazole  (EXP)
ethanol  (EXP,ISO)
fasudil  (EXP)
finasteride  (EXP)
fluoxetine  (EXP,ISO)
flutamide  (EXP)
folic acid  (ISO)
fonofos  (ISO)
fulvestrant  (ISO)
gamma-tocopherol  (ISO)
glucose  (EXP)
Honokiol  (EXP)
hydralazine  (ISO)
hydrogen peroxide  (ISO)
hydroxyl  (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,ISO)
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)
oxidopamine  (EXP)
ozone  (EXP,ISO)
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)
poly(vinylpyrrolidone)  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
Pyridostigmine bromide  (ISO)
pyrimidifen  (ISO)
pyrrolidine dithiocarbamate  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP,ISO)
SB 415286  (EXP)
scopolamine  (EXP,ISO)
sevoflurane  (EXP,ISO)
silver atom  (EXP)
silver(0)  (EXP)
silver(1+) nitrate  (ISO)
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)
U-73122  (EXP)
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 - curated
# Reference Title Reference Citation
1. The SNARE Vti1a-beta is localized to small synaptic vesicles and participates in a novel SNARE complex. Antonin W, etal., J Neurosci 2000 Aug 1;20(15):5724-32.
2. The synaptophysin-encoding gene in rat and man is specifically transcribed in neuroendocrine cells. Bargou RC and Leube RE, Gene 1991 Mar 15;99(2):197-204.
3. Cellugyrin and synaptogyrin facilitate targeting of synaptophysin to a ubiquitous synaptic vesicle-sized compartment in PC12 cells. Belfort GM and Kandror KV, J Biol Chem. 2003 Nov 28;278(48):47971-8. Epub 2003 Aug 18.
4. Changed clathrin regulatory proteins in the brains of Alzheimer's disease patients and animal models. Cao Y, etal., J Alzheimers Dis. 2010;22(1):329-42. doi: 10.3233/JAD-2010-100162.
5. Piccolo, a presynaptic zinc finger protein structurally related to bassoon. Fenster SD, etal., Neuron 2000 Jan;25(1):203-14.
6. The V0 sector of the V-ATPase, synaptobrevin, and synaptophysin are associated on synaptic vesicles in a Triton X-100-resistant, freeze-thawing sensitive, complex. Galli T, etal., J Biol Chem. 1996 Jan 26;271(4):2193-8.
7. 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.
8. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
9. Increased synaptophysin expression through whisker stimulation in rat. Ishibashi H Cell Mol Neurobiol 2002 Apr;22(2):191-5.
10. Characterization of a multidomain adaptor protein, p140Cap, as part of a pre-synaptic complex. 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. Sept8 controls the binding of vesicle-associated membrane protein 2 to synaptophysin. Ito H, etal., J Neurochem. 2009 Feb;108(4):867-80. doi: 10.1111/j.1471-4159.2008.05849.x.
12. A 38,000-dalton membrane protein (p38) present in synaptic vesicles. Jahn R, etal., Proc Natl Acad Sci U S A. 1985 Jun;82(12):4137-41.
13. Synaptic adhesion molecule IgSF11 regulates synaptic transmission and plasticity. Jang S, etal., Nat Neurosci. 2016 Jan;19(1):84-93. doi: 10.1038/nn.4176. Epub 2015 Nov 23.
14. Neuroligin-1 performs neurexin-dependent and neurexin-independent functions in synapse validation. Ko J, etal., EMBO J. 2009 Oct 21;28(20):3244-55. doi: 10.1038/emboj.2009.249. Epub 2009 Sep 3.
15. Synaptophysin: molecular organization and mRNA expression as determined from cloned cDNA. Leube RE, etal., EMBO J 1987 Nov;6(11):3261-8.
16. A Bcl-xL-Drp1 complex regulates synaptic vesicle membrane dynamics during endocytosis. Li H, etal., Nat Cell Biol. 2013 Jul;15(7):773-85. doi: 10.1038/ncb2791. Epub 2013 Jun 23.
17. Activity-dependent changes in synaptophysin immunoreactivity in hippocampus, piriform cortex, and entorhinal cortex of the rat. Li S, etal., Neuroscience 2002;115(4):1221-9.
18. Interaction of the mu-opioid receptor with synaptophysin influences receptor trafficking and signaling. Liang YJ, etal., Mol Pharmacol. 2007 Jan;71(1):123-31. Epub 2006 Sep 27.
19. A plethora of presynaptic proteins associated with ATP-storing organelles in cultured astrocytes. Maienschein V, etal., Glia. 1999 May;26(3):233-44.
20. Identification and characterization of the BRI2 interactome in the brain. Martins F, etal., Sci Rep. 2018 Feb 23;8(1):3548. doi: 10.1038/s41598-018-21453-3.
21. Complexins: cytosolic proteins that regulate SNAP receptor function. McMahon HT, etal., Cell 1995 Oct 6;83(1):111-9.
22. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
23. Regulation of synaptic structure and function by palmitoylated AMPA receptor binding protein. Misra C, etal., Mol Cell Neurosci. 2010 Apr;43(4):341-52. Epub 2010 Jan 18.
24. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
26. Fluorescence resonance energy transfer detection of synaptophysin I and vesicle-associated membrane protein 2 interactions during exocytosis from single live synapses. Pennuto M, etal., Mol Biol Cell. 2002 Aug;13(8):2706-17.
27. GOA pipeline RGD automated data pipeline
28. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
29. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
30. Evidence for early endosome-like fusion of recently endocytosed synaptic vesicles. Rizzoli SO, etal., Traffic. 2006 Sep;7(9):1163-76.
31. Grb4 and GIT1 transduce ephrinB reverse signals modulating spine morphogenesis and synapse formation. Segura I, etal., Nat Neurosci. 2007 Mar;10(3):301-10. Epub 2007 Feb 18.
32. The cDNA and derived amino acid sequences for rat and human synaptophysin. Sudhof TC, etal., Nucleic Acids Res 1987 Nov 25;15(22):9607.
33. Regulation of synaptophysin degradation by mammalian homologues of seven in absentia. Wheeler TC, etal., J Biol Chem 2002 Mar 22;277(12):10273-82.
34. 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: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   PMID:35715368  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.2X14,849,444 - 14,864,553 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX14,849,444 - 14,864,745 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX19,663,795 - 19,678,920 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X20,404,212 - 20,419,339 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0X16,669,360 - 16,684,482 (+)NCBIRnor_WKY
Rnor_6.0X15,694,699 - 15,709,244 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,695,566 - 15,707,436 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X16,485,963 - 16,501,050 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,890,307 - 26,905,319 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X26,943,775 - 26,958,788 (-)NCBI
CeleraX14,932,808 - 14,947,852 (-)NCBICelera
Cytogenetic MapXq12NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh38X49,187,815 - 49,200,193 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 EnsemblX49,187,815 - 49,200,218 (-)EnsemblGRCh38hg38GRCh38
GRCh37X49,044,268 - 49,056,652 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,931,209 - 48,943,605 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X48,800,635 - 48,813,032NCBI
CeleraX52,607,708 - 52,620,104 (+)NCBICelera
Cytogenetic MapXp11.23NCBI
HuRefX46,701,336 - 46,713,608 (-)NCBIHuRef
CHM1_1X49,076,586 - 49,088,982 (-)NCBICHM1_1
T2T-CHM13v2.0X48,599,669 - 48,612,053 (-)NCBIT2T-CHM13v2.0
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm39X7,504,819 - 7,519,495 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX7,504,710 - 7,519,495 (+)EnsemblGRCm39 Ensembl
GRCm38X7,638,580 - 7,653,256 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX7,638,471 - 7,653,256 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X7,215,706 - 7,230,382 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X6,795,670 - 6,810,210 (+)NCBIMGSCv36mm8
CeleraX3,817,995 - 3,833,335 (-)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.44NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_004955543675,294 - 689,686 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955543675,294 - 689,579 (-)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
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_v0Mhudiblu_PPA_v0panPan3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X42,429,161 - 42,441,205 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX42,429,165 - 42,441,152 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X42,413,127 - 42,425,154 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X42,400,777 - 42,412,809 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X42,495,540 - 42,507,567 (-)NCBIUU_Cfam_GSD_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2X34,821,818 - 34,835,592 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367211,062,217 - 1,075,988 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049367211,062,206 - 1,075,935 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 EnsemblX43,232,192 - 43,246,680 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X43,232,190 - 43,246,764 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X48,080,132 - 48,094,682 (-)NCBISscrofa10.2Sscrofa10.2susScr3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.1X46,287,610 - 46,299,926 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX46,287,282 - 46,299,773 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607611,848,275 - 11,860,485 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_004624893928,099 - 942,903 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624893929,460 - 942,806 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Syp
38 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:603
Count of miRNA genes:273
Interacting mature miRNAs:342
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 (
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)
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)X143491017Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,865,458 - 14,865,602 (+)MAPPERmRatBN7.2
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
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,865,545 - 14,865,582 (+)MAPPERmRatBN7.2
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
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,849,483 - 14,849,685 (+)MAPPERmRatBN7.2
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
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,853,579 - 14,853,917 (+)MAPPERmRatBN7.2
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


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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000085907   ⟹   ENSRNOP00000075360
RefSeq Status:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,849,444 - 14,863,988 (-)Ensembl
Rnor_6.0 EnsemblX15,695,566 - 15,707,436 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107562   ⟹   ENSRNOP00000096197
RefSeq Status:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,849,444 - 14,864,745 (-)Ensembl
RefSeq Acc Id: NM_012664   ⟹   NP_036796
RefSeq Status: VALIDATED
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
Reference Sequences
RefSeq Acc Id: NP_036796   ⟸   NM_012664
- UniProtKB: Q499R3 (UniProtKB/Swiss-Prot),   P07825 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075360   ⟸   ENSRNOT00000085907
RefSeq Acc Id: ENSRNOP00000096197   ⟸   ENSRNOT00000107562
Protein Domains

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P07825-F1-model_v2 AlphaFold P07825 1-307 view protein structure


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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3802 AgrOrtholog
BioCyc Gene G2FUF-2909 BioCyc
Ensembl Genes ENSRNOG00000059720 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000075360.2 UniProtKB/TrEMBL
  ENSRNOP00000096197.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000085907.2 UniProtKB/TrEMBL
  ENSRNOT00000107562.1 UniProtKB/TrEMBL
InterPro Marvel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synaptophysin/porin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24804 UniProtKB/Swiss-Prot
PANTHER PTHR10306 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10306:SF10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam MARVEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Syp PhenoGen
  SYNAPTOP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYPH_RAT 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