Syt4 (synaptotagmin 4) - Rat Genome Database

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Gene: Syt4 (synaptotagmin 4) Rattus norvegicus
Analyze
Symbol: Syt4
Name: synaptotagmin 4
RGD ID: 68397
Description: Enables several functions, including phosphatidylserine binding activity; protein dimerization activity; and syntaxin binding activity. Involved in several processes, including dense core granule cytoskeletal transport; negative regulation of transport; and vesicle organization. Located in several cellular components, including astrocyte projection; neuronal cell body; and secretory vesicle. Orthologous to human SYT4 (synaptotagmin 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: synaptotagmin IV; synaptotagmin-4; sytIV
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81823,311,454 - 23,320,863 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1823,312,859 - 23,320,815 (-)EnsemblGRCr8
mRatBN7.21823,036,973 - 23,046,380 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1823,038,378 - 23,046,332 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1823,165,351 - 23,174,758 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01823,922,462 - 23,931,883 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01823,260,316 - 23,269,724 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01824,172,580 - 24,181,989 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1824,172,587 - 24,182,012 (-)Ensemblrn6Rnor6.0
Rnor_5.01823,893,019 - 23,902,428 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41823,805,080 - 23,814,489 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1822,798,742 - 22,808,151 (-)NCBICelera
RGSC_v3.11823,833,130 - 23,841,087 (-)NCBI
Cytogenetic Map18p12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
calcium-dependent activation of synaptic vesicle fusion  (IBA)
calcium-ion regulated exocytosis  (NAS)
cell differentiation  (IEA)
dense core granule cytoskeletal transport  (IEA,IMP,ISO)
insulin secretion involved in cellular response to glucose stimulus  (IMP)
memory  (IEA,ISO)
negative regulation of calcium ion-dependent exocytosis  (IDA)
negative regulation of catecholamine secretion  (IEA,IGI,ISO)
negative regulation of dense core granule exocytosis  (IMP)
negative regulation of neurotransmitter secretion  (IDA)
negative regulation of protein secretion  (IEA,ISO)
negative regulation of retrograde trans-synaptic signaling by neuropeptide  (IEA,ISO)
negative regulation of short-term neuronal synaptic plasticity  (IEA,ISO)
negative regulation of synaptic vesicle exocytosis  (IEA,ISO)
negative regulation of vesicle fusion  (IDA)
neurotransmitter secretion  (ISO,NAS)
positive regulation of dendrite extension  (ISO)
positive regulation of dense core granule exocytosis  (IEA,ISO)
positive regulation of glutamate secretion  (IEA,ISO)
regulation of calcium ion-dependent exocytosis  (IBA,IEA,ISO)
regulation of dopamine secretion  (IEA,ISO)
regulation of endocytosis  (IEA,IMP,ISO)
regulation of postsynaptic dense core vesicle exocytosis  (IEA,ISO)
regulation of trans-synaptic signaling by BDNF, modulating synaptic transmission  (IEA,ISO)
regulation of vesicle fusion  (IEA,IMP,ISO)
secretory granule maturation  (IMP)
vesicle fusion  (IBA)
vesicle fusion with vesicle  (IMP)
vesicle-mediated transport  (IBA)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Synaptotagmin IV is necessary for the maturation of secretory granules in PC12 cells. Ahras M, etal., J Cell Biol. 2006 Apr 24;173(2):241-51. Epub 2006 Apr 17.
2. Reduced insulin secretion correlates with decreased expression of exocytotic genes in pancreatic islets from patients with type 2 diabetes. Andersson SA, etal., Mol Cell Endocrinol. 2012 Nov 25;364(1-2):36-45. doi: 10.1016/j.mce.2012.08.009. Epub 2012 Aug 23.
3. Analysis of the synaptotagmin family during reconstituted membrane fusion. Uncovering a class of inhibitory isoforms. Bhalla A, etal., J Biol Chem. 2008 Aug 1;283(31):21799-807. doi: 10.1074/jbc.M709628200. Epub 2008 May 28.
4. Capture of Dense Core Vesicles at Synapses by JNK-Dependent Phosphorylation of Synaptotagmin-4. Bharat V, etal., Cell Rep. 2017 Nov 21;21(8):2118-2133. doi: 10.1016/j.celrep.2017.10.084.
5. Delineation of the oligomerization, AP-2 binding, and synprint binding region of the C2B domain of synaptotagmin. Chapman ER, etal., J Biol Chem. 1998 Dec 4;273(49):32966-72.
6. Variations of synaptotagmin I, synaptotagmin IV, and synaptophysin mRNA levels in rat hippocampus during the estrous cycle. Crispino M, etal., Exp Neurol 1999 Oct;159(2):574-83.
7. Structural basis for the evolutionary inactivation of Ca2+ binding to synaptotagmin 4. Dai H, etal., Nat Struct Mol Biol 2004 Sep;11(9):844-9. Epub 2004 Aug 15.
8. Synthesis degradation, and subcellular localization of synaptotagmin IV, a neuronal immediate early gene product. Ferguson GD, etal., J Neurochem. 1999 May;72(5):1821-31.
9. Nerve growth factor-dependent sorting of synaptotagmin IV protein to mature dense-core vesicles that undergo calcium-dependent exocytosis in PC12 cells. Fukuda M, etal., J Biol Chem 2003 Jan 31;278(5):3220-6. Epub 2002 Nov 21.
10. 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.
11. Synaptotagmin IV is present at the Golgi and distal parts of neurites. Ibata K, etal., J Neurochem. 2000 Feb;74(2):518-26.
12. Ca(2+)-dependent and -independent activities of neural and non-neural synaptotagmins. Li C, etal., Nature 1995 Jun 15;375(6532):594-9.
13. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
14. Upregulation of synaptotagmin IV inhibits transmitter release in PC12 cells with targeted synaptotagmin I knockdown. Moore-Dotson JM, etal., BMC Neurosci. 2010 Aug 24;11:104. doi: 10.1186/1471-2202-11-104.
15. JNK phosphorylates synaptotagmin-4 and enhances Ca2+-evoked release. Mori Y, etal., EMBO J. 2008 Jan 9;27(1):76-87. Epub 2007 Nov 29.
16. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. GOA pipeline RGD automated data pipeline
18. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
20. Regulation of KIF1A-Driven Dense Core Vesicle Transport: Ca2+/CaM Controls DCV Binding and Liprin-α/TANC2 Recruits DCVs to Postsynaptic Sites. Stucchi R, etal., Cell Rep. 2018 Jul 17;24(3):685-700. doi: 10.1016/j.celrep.2018.06.071.
21. Functional and biochemical analysis of the C2 domains of synaptotagmin IV. Thomas DM, etal., Mol Biol Cell. 1999 Jul;10(7):2285-95.
22. Two synaptotagmin genes, Syt1 and Syt4, are differentially regulated in adult brain and during postnatal development following kainic acid-induced seizures. Tocco G, etal., Brain Res Mol Brain Res 1996 Sep 1;40(2):229-39.
23. Upregulation and axonal transport of synaptotagmin-IV in the direct-pathway medium spiny neurons in hemi-parkinsonian rats induced by dopamine D1 receptor stimulation. Tratnjek L, etal., Eur J Neurosci. 2016 Apr;43(7):885-98. doi: 10.1111/ejn.13161. Epub 2016 Feb 23.
24. Functional properties of multiple synaptotagmins in brain. Ullrich B, etal., Neuron 1994 Dec;13(6):1281-91.
25. Synaptotagmin IV is an immediate early gene induced by depolarization in PC12 cells and in brain. Vician L, etal., Proc Natl Acad Sci U S A 1995 Mar 14;92(6):2164-8.
26. Rat and Drosophila synaptotagmin 4 have opposite effects during SNARE-catalyzed membrane fusion. Wang Z and Chapman ER, J Biol Chem. 2010 Oct 1;285(40):30759-66. doi: 10.1074/jbc.M110.137745. Epub 2010 Aug 5.
27. The synaptotagmins: calcium sensors for vesicular trafficking. Yoshihara M and Montana ES, Neuroscientist. 2004 Dec;10(6):566-74.
28. Synaptotagmin IV regulates glial glutamate release. Zhang Q, etal., Proc Natl Acad Sci U S A. 2004 Jun 22;101(25):9441-6. Epub 2004 Jun 14.
29. Synaptotagmin IV modulation of vesicle size and fusion pores in PC12 cells. Zhang Z, etal., Biophys J. 2010 Mar 17;98(6):968-78. doi: 10.1016/j.bpj.2009.11.024.
30. Release mode of large and small dense-core vesicles specified by different synaptotagmin isoforms in PC12 cells. Zhang Z, etal., Mol Biol Cell. 2011 Jul 1;22(13):2324-36. doi: 10.1091/mbc.E11-02-0159. Epub 2011 May 5.
Additional References at PubMed
PMID:8626542   PMID:12060780   PMID:12135783   PMID:15390175   PMID:15496596   PMID:16407532   PMID:18468511   PMID:19103603   PMID:19136969   PMID:19448629   PMID:20010821   PMID:21287204  
PMID:21576241   PMID:22695963   PMID:23999003   PMID:28254618  


Genomics

Comparative Map Data
Syt4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81823,311,454 - 23,320,863 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1823,312,859 - 23,320,815 (-)EnsemblGRCr8
mRatBN7.21823,036,973 - 23,046,380 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1823,038,378 - 23,046,332 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1823,165,351 - 23,174,758 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01823,922,462 - 23,931,883 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01823,260,316 - 23,269,724 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01824,172,580 - 24,181,989 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1824,172,587 - 24,182,012 (-)Ensemblrn6Rnor6.0
Rnor_5.01823,893,019 - 23,902,428 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41823,805,080 - 23,814,489 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1822,798,742 - 22,808,151 (-)NCBICelera
RGSC_v3.11823,833,130 - 23,841,087 (-)NCBI
Cytogenetic Map18p12NCBI
SYT4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381843,267,892 - 43,277,490 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1843,267,892 - 43,277,535 (-)Ensemblhg38GRCh38
GRCh371840,847,857 - 40,857,455 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361839,101,855 - 39,111,342 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341839,101,856 - 39,111,342NCBI
Celera1837,656,042 - 37,665,799 (-)NCBICelera
Cytogenetic Map18q12.3NCBI
HuRef1837,706,367 - 37,716,125 (-)NCBIHuRef
CHM1_11840,774,888 - 40,784,646 (-)NCBICHM1_1
T2T-CHM13v2.01843,459,665 - 43,469,261 (-)NCBIT2T-CHM13v2.0
Syt4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391831,570,861 - 31,580,468 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1831,570,861 - 31,580,459 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381831,437,808 - 31,447,415 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1831,437,808 - 31,447,406 (-)Ensemblmm10GRCm38
MGSCv371831,597,462 - 31,607,069 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361831,580,818 - 31,590,425 (-)NCBIMGSCv36mm8
Celera1831,923,439 - 31,933,127 (-)NCBICelera
Cytogenetic Map18B1NCBI
cM Map1817.75NCBI
Syt4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540229,193,455 - 29,204,975 (-)Ensembl
ChiLan1.0NW_00495540229,195,124 - 29,204,816 (-)NCBIChiLan1.0ChiLan1.0
SYT4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21760,684,036 - 60,693,728 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11846,376,629 - 46,386,310 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01836,540,756 - 36,550,439 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11840,089,938 - 40,099,721 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1840,089,938 - 40,099,721 (-)EnsemblpanPan2panpan1.1
SYT4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1747,555,110 - 47,565,313 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl747,509,852 - 47,563,714 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha746,971,902 - 46,982,069 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0747,511,288 - 47,521,437 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl747,511,232 - 47,521,424 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1747,213,662 - 47,223,814 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0747,249,749 - 47,259,895 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0747,539,197 - 47,549,385 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Syt4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494443,708,440 - 43,718,775 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365173,035,521 - 3,047,964 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365173,035,840 - 3,044,065 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYT4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6127,382,263 - 127,392,164 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.16127,382,248 - 127,392,258 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SYT4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11837,595,187 - 37,604,931 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1837,595,035 - 37,606,007 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605012,024,554 - 12,034,291 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Syt4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477917,592,669 - 17,603,403 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462477917,593,760 - 17,603,217 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Syt4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11542,358,362 - 42,367,739 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Syt4
48 total Variants
miRNA Target Status (No longer updated)

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir30erno-miR-30e-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir30arno-miR-30a-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir292rno-miR-292-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830

Predicted Target Of
Summary Value
Count of predictions:339
Count of miRNA genes:196
Interacting mature miRNAs:256
Transcripts:ENSRNOT00000023594
Prediction methods:Miranda, 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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301410Bp317Blood pressure QTL 3170.004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181221923726822399Rat
2301409Cm70Cardiac mass QTL 700.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)18706572852065728Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)182201556261600538Rat
1331735Rf44Renal function QTL 442.981urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181564228031610627Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181221668431644508Rat
12904716Am21Aortic mass QTL 210.005aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)18706572852065728Rat
8552968Pigfal19Plasma insulin-like growth factor 1 level QTL 1911.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)18126032889Rat
12904714Cm131Cardiac mass QTL 1310.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)18706572852065728Rat
12904715Cm132Cardiac mass QTL 1320.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)18706572852065728Rat
1331781Scl28Serum cholesterol level QTL 283.995blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)18125071266Rat
6903345Bp349Blood pressure QTL 3493.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18391722648917226Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181522610142690662Rat
6903347Bp350Blood pressure QTL 3504.4arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18131610627Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18546045542690191Rat
6903349Bp351Blood pressure QTL 3513.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18391722648917226Rat
6903351Bp352Blood pressure QTL 3523.3arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18391722648917226Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18131610627Rat
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181221668431644508Rat
1331775Bp235Blood pressure QTL 2353.201arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181564228031610627Rat
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18144930869Rat
12904680Bw189Body weight QTL 1890.019body mass (VT:0001259)body weight (CMO:0000012)181221923726822399Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181955353285493247Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181206648257066482Rat
1641910Colcr3Colorectal carcinoma resistance QTL 35.020.000007intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)18125022372Rat
12904693Am20Aortic mass QTL 200.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)181221923726822399Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181206648285493247Rat
12904695Kidm73Kidney mass QTL 730.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)181221923726822399Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18381190230809809Rat
12904689Cm128Cardiac mass QTL 1280.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)181221923726822399Rat
12904690Cm129Cardiac mass QTL 1290.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)181221923726822399Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134566578Rat
12904691Cm130Cardiac mass QTL 1300.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)181221923726822399Rat
9590248Scort10Serum corticosterone level QTL 1019.710.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)18126032889Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18448264849482648Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18154490981Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181206648285493247Rat
11565454Kidm59Kidney mass QTL 590.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)18706572852065728Rat
1331754Bp230Blood pressure QTL 2304.61609arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181564228086134022Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134566578Rat
61375Bp41Blood pressure QTL 412.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)18430735449307354Rat

Markers in Region
RH139264  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21823,037,125 - 23,037,316 (+)MAPPERmRatBN7.2
Rnor_6.01824,172,733 - 24,172,923NCBIRnor6.0
Rnor_5.01823,893,172 - 23,893,362UniSTSRnor5.0
RGSC_v3.41823,805,233 - 23,805,423UniSTSRGSC3.4
Celera1822,798,895 - 22,799,085UniSTS
RH 3.4 Map18277.0UniSTS
Cytogenetic Map18p12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
13 9 36 151 55 49 24 57 24 4 195 116 5 137 34 79 25 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000023594   ⟹   ENSRNOP00000023593
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1823,312,859 - 23,320,815 (-)Ensembl
mRatBN7.2 Ensembl1823,038,378 - 23,046,332 (-)Ensembl
Rnor_6.0 Ensembl1824,172,587 - 24,182,012 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000110395   ⟹   ENSRNOP00000097035
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1823,312,859 - 23,318,582 (-)Ensembl
mRatBN7.2 Ensembl1823,038,378 - 23,044,101 (-)Ensembl
RefSeq Acc Id: NM_031693   ⟹   NP_113881
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81823,311,454 - 23,320,863 (-)NCBI
mRatBN7.21823,036,973 - 23,046,380 (-)NCBI
Rnor_6.01824,172,580 - 24,181,989 (-)NCBI
Rnor_5.01823,893,019 - 23,902,428 (-)NCBI
RGSC_v3.41823,805,080 - 23,814,489 (-)RGD
Celera1822,798,742 - 22,808,151 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_113881 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA67327 (Get FASTA)   NCBI Sequence Viewer  
  AAA68519 (Get FASTA)   NCBI Sequence Viewer  
  ABA00483 (Get FASTA)   NCBI Sequence Viewer  
  EDL76165 (Get FASTA)   NCBI Sequence Viewer  
  EDL76166 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000023593
  ENSRNOP00000023593.4
GenBank Protein P50232 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_113881   ⟸   NM_031693
- UniProtKB: P50232 (UniProtKB/Swiss-Prot),   A6J2N4 (UniProtKB/TrEMBL),   Q3S2E5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000023593   ⟸   ENSRNOT00000023594
Ensembl Acc Id: ENSRNOP00000097035   ⟸   ENSRNOT00000110395
Protein Domains
C2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P50232-F1-model_v2 AlphaFold P50232 1-425 view protein structure

Transcriptome

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

Promoters
RGD ID:13700671
Promoter ID:EPDNEW_R11195
Type:initiation region
Name:Syt4_1
Description:synaptotagmin 4
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_6.01824,181,941 - 24,182,001EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68397 AgrOrtholog
BioCyc Gene G2FUF-8063 BioCyc
Ensembl Genes ENSRNOG00000017333 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000023594 ENTREZGENE
  ENSRNOT00000023594.6 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot
InterPro C2_dom UniProtKB/Swiss-Prot
  C2_domain_sf UniProtKB/Swiss-Prot
  Synaptotagmin UniProtKB/Swiss-Prot
KEGG Report rno:64440 UniProtKB/Swiss-Prot
NCBI Gene 64440 ENTREZGENE
PANTHER PTHR10024:SF114 UniProtKB/Swiss-Prot
  SYNAPTOTAGMIN UniProtKB/Swiss-Prot
Pfam PF00168 UniProtKB/Swiss-Prot
PhenoGen Syt4 PhenoGen
PRINTS SYNAPTOTAGMN UniProtKB/Swiss-Prot
PROSITE PS50004 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000017333 RatGTEx
SMART SM00239 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49562 UniProtKB/Swiss-Prot
UniProt A0A8I6AR88_RAT UniProtKB/TrEMBL
  A6J2N4 ENTREZGENE, UniProtKB/TrEMBL
  P50232 ENTREZGENE
  Q3S2E5 ENTREZGENE, UniProtKB/TrEMBL
  SYT4_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Syt4  synaptotagmin 4  Syt4  synaptotagmin IV  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Syt4  synaptotagmin IV    synaptotagmin 4  Name updated 1299863 APPROVED
2002-06-10 Syt4  synaptotagmin 4      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease expression increases in some regions of th brain in response to kainic acid-induced seizures 730127
gene_function binds to clathrin-adaptor protein AP-2 with high affinity 68205
gene_regulation mRNA accumulation induced in PC12 cells by potassium depolarization, calcium ionophore, ATP, and forskolin 730180