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. Biomarker of visual epilepsy. 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81823,311,454 - 23,320,863 (-)NCBIGRCr8
mRatBN7.21823,036,973 - 23,046,380 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1823,038,378 - 23,046,332 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1823,165,351 - 23,174,758 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01823,922,462 - 23,931,883 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01823,260,316 - 23,269,724 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01824,172,580 - 24,181,989 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1824,172,587 - 24,182,012 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01823,893,019 - 23,902,428 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41823,805,080 - 23,814,489 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11823,833,130 - 23,841,087 (-)NCBI
Celera1822,798,742 - 22,808,151 (-)NCBICelera
Cytogenetic Map18p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. Synaptotagmin IV is present at the Golgi and distal parts of neurites. Ibata K, etal., J Neurochem. 2000 Feb;74(2):518-26.
11. Ca(2+)-dependent and -independent activities of neural and non-neural synaptotagmins. Li C, etal., Nature 1995 Jun 15;375(6532):594-9.
12. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
13. 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.
14. 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.
15. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. GOA pipeline RGD automated data pipeline
17. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
19. 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.
20. Functional and biochemical analysis of the C2 domains of synaptotagmin IV. Thomas DM, etal., Mol Biol Cell. 1999 Jul;10(7):2285-95.
21. 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.
22. 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.
23. Functional properties of multiple synaptotagmins in brain. Ullrich B, etal., Neuron 1994 Dec;13(6):1281-91.
24. 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.
25. 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.
26. The synaptotagmins: calcium sensors for vesicular trafficking. Yoshihara M and Montana ES, Neuroscientist. 2004 Dec;10(6):566-74.
27. 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.
28. 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.
29. 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 (-)NCBIGRCr8
mRatBN7.21823,036,973 - 23,046,380 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1823,038,378 - 23,046,332 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1823,165,351 - 23,174,758 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01823,922,462 - 23,931,883 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01823,260,316 - 23,269,724 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01824,172,580 - 24,181,989 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1824,172,587 - 24,182,012 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01823,893,019 - 23,902,428 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41823,805,080 - 23,814,489 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11823,833,130 - 23,841,087 (-)NCBI
Celera1822,798,742 - 22,808,151 (-)NCBICelera
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 (-)EnsemblGRCh38hg38GRCh38
GRCh371840,847,857 - 40,857,455 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361839,101,855 - 39,111,342 (-)NCBINCBI36Build 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 Ensembl
GRCm381831,437,808 - 31,447,415 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1831,437,808 - 31,447,406 (-)EnsemblGRCm38mm10GRCm38
MGSCv371831,597,462 - 31,607,069 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha746,971,902 - 46,982,069 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0747,511,288 - 47,521,437 (+)NCBIROS_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_1.0
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477917,593,760 - 17,603,217 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Syt4
26 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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)18125758124Rat
9590248Scort10Serum corticosterone level QTL 1019.710.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)18125758124Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18130558703Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134291613Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134291613Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135374722Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18142547119Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18420794160377792Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18518585840503530Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181179151863636873Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181179151883218561Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181179151883218561Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194179131393320Rat
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181194179131393320Rat
12904690Cm129Cardiac mass QTL 1290.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)181194427326548295Rat
12904689Cm128Cardiac mass QTL 1280.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)181194427326548295Rat
12904693Am20Aortic mass QTL 200.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)181194427326548295Rat
12904695Kidm73Kidney mass QTL 730.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)181194427326548295Rat
12904691Cm130Cardiac mass QTL 1300.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)181194427326548295Rat
12904680Bw189Body weight QTL 1890.019body mass (VT:0001259)body weight (CMO:0000012)181194427326548295Rat
2301410Bp317Blood pressure QTL 3170.004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181194427326548295Rat
1331781Scl28Serum cholesterol level QTL 283.995blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)181194429924797117Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181194429931359530Rat
61375Bp41Blood pressure QTL 412.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)181194429941122201Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194429952293055Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181194429959330563Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194454459796478Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181495133759951337Rat
1358193Emca2Estrogen-induced mammary cancer QTL 21.6mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)181800759963571040Rat
1331735Rf44Renal function QTL 442.981urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181823456431359530Rat
1331775Bp235Blood pressure QTL 2353.201arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181823456431359530Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181927890183218561Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182137289383213037Rat
1641923Colcr8Colorectal carcinoma resistance QTL 83.10.0014intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)182206624252293055Rat

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
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 70
Low 3 4 12 4 4 4 16 25 2
Below cutoff 18 15 8 14 8 8 8 4 12 7 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000023594   ⟹   ENSRNOP00000023593
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1823,038,378 - 23,046,332 (-)Ensembl
Rnor_6.0 Ensembl1824,172,587 - 24,182,012 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110395   ⟹   ENSRNOP00000097035
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
Reference Protein Sequences
RefSeq Acc Id: NP_113881   ⟸   NM_031693
- UniProtKB: P50232 (UniProtKB/Swiss-Prot),   A6J2N4 (UniProtKB/TrEMBL),   Q3S2E5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000023593   ⟸   ENSRNOT00000023594
RefSeq 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, UniProtKB/TrEMBL
  ENSRNOG00055024114 UniProtKB/Swiss-Prot
  ENSRNOG00060026793 UniProtKB/Swiss-Prot
  ENSRNOG00065012162 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000023594 ENTREZGENE
  ENSRNOT00000023594.6 UniProtKB/Swiss-Prot
  ENSRNOT00000110395.1 UniProtKB/TrEMBL
  ENSRNOT00055041439 UniProtKB/Swiss-Prot
  ENSRNOT00060046438 UniProtKB/Swiss-Prot
  ENSRNOT00065019770 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro C2_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synaptotagmin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64440 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 64440 ENTREZGENE
PANTHER PTHR10024:SF114 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYNAPTOTAGMIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PF00168 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Syt4 PhenoGen
PRINTS SYNAPTOTAGMN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PS50004 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000017333 RatGTEx
  ENSRNOG00055024114 RatGTEx
  ENSRNOG00060026793 RatGTEx
  ENSRNOG00065012162 RatGTEx
SMART SM00239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49562 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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