Syt10 (synaptotagmin 10) - Rat Genome Database

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Gene: Syt10 (synaptotagmin 10) Rattus norvegicus
Analyze
Symbol: Syt10
Name: synaptotagmin 10
RGD ID: 62041
Description: Predicted to enable several functions, including calcium ion binding activity; phospholipid binding activity; and protein dimerization activity. Predicted to be involved in positive regulation of calcium ion-dependent exocytosis; presynaptic dense core vesicle exocytosis; and sensory perception of smell. Predicted to be located in synaptic vesicle membrane. Predicted to be active in several cellular components, including exocytic vesicle; glutamatergic synapse; and presynapse. Biomarker of visual epilepsy. Orthologous to human SYT10 (synaptotagmin 10); INTERACTS WITH 17beta-estradiol; ammonium chloride; bis(2-ethylhexyl) phthalate.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: synaptotagmin X; synaptotagmin-10; sytX
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87122,737,301 - 122,800,462 (-)NCBIGRCr8
mRatBN7.27120,857,698 - 120,920,863 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7120,862,972 - 120,920,863 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7122,661,274 - 122,718,960 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07124,887,410 - 124,945,103 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07124,819,888 - 124,879,596 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07130,769,039 - 130,827,030 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7130,768,841 - 130,827,152 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07130,452,003 - 130,510,388 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47128,115,443 - 128,174,355 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17128,149,672 - 128,208,585 (-)NCBI
Celera7117,334,018 - 117,391,703 (-)NCBICelera
Cytogenetic Map7q34NCBI
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

References

References - curated
# Reference Title Reference Citation
1. A novel seizure-induced synaptotagmin gene identified by differential display. Babity JM, etal., Proc Natl Acad Sci U S A 1997 Mar 18;94(6):2638-41.
2. 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.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10531343   PMID:10531344   PMID:12860971   PMID:21496647  


Genomics

Comparative Map Data
Syt10
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87122,737,301 - 122,800,462 (-)NCBIGRCr8
mRatBN7.27120,857,698 - 120,920,863 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7120,862,972 - 120,920,863 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7122,661,274 - 122,718,960 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07124,887,410 - 124,945,103 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07124,819,888 - 124,879,596 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07130,769,039 - 130,827,030 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7130,768,841 - 130,827,152 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07130,452,003 - 130,510,388 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47128,115,443 - 128,174,355 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17128,149,672 - 128,208,585 (-)NCBI
Celera7117,334,018 - 117,391,703 (-)NCBICelera
Cytogenetic Map7q34NCBI
SYT10
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381233,374,238 - 33,439,819 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1233,374,238 - 33,439,819 (-)EnsemblGRCh38hg38GRCh38
GRCh371233,527,173 - 33,592,754 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361233,419,615 - 33,484,021 (-)NCBINCBI36Build 36hg18NCBI36
Build 341233,419,614 - 33,484,021NCBI
Celera1213,335,630 - 13,400,035 (-)NCBICelera
Cytogenetic Map12p11.1NCBI
HuRef1233,268,030 - 33,332,379 (-)NCBIHuRef
CHM1_11233,493,388 - 33,557,762 (-)NCBICHM1_1
T2T-CHM13v2.01233,245,435 - 33,311,036 (-)NCBIT2T-CHM13v2.0
Syt10
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391589,657,221 - 89,726,181 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1589,666,596 - 89,726,063 (-)EnsemblGRCm39 Ensembl
GRCm381589,773,714 - 89,841,980 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1589,782,393 - 89,841,860 (-)EnsemblGRCm38mm10GRCm38
MGSCv371589,612,824 - 89,672,291 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361589,610,160 - 89,669,536 (-)NCBIMGSCv36mm8
Celera1591,906,236 - 91,966,102 (-)NCBICelera
Cytogenetic Map15E3NCBI
cM Map1544.96NCBI
Syt10
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555052,403,055 - 2,449,528 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555052,392,086 - 2,449,528 (+)NCBIChiLan1.0ChiLan1.0
SYT10
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21063,284,958 - 63,358,857 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11263,286,586 - 63,355,247 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01252,761,294 - 52,830,221 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11255,364,858 - 55,429,298 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1255,364,714 - 55,429,298 (+)Ensemblpanpan1.1panPan2
SYT10
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12715,593,709 - 15,657,184 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2715,593,649 - 15,687,920 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2730,768,616 - 30,835,595 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02715,771,897 - 15,835,539 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2715,771,596 - 15,866,288 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12715,579,522 - 15,646,934 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02715,608,782 - 15,676,039 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02730,916,635 - 30,980,314 (-)NCBIUU_Cfam_GSD_1.0
Syt10
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494576,107,495 - 76,166,270 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366072,940,466 - 2,994,344 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366072,940,607 - 2,995,178 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYT10
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl540,872,283 - 40,934,326 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1540,869,418 - 40,940,851 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2543,998,608 - 44,061,673 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SYT10
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11132,846,425 - 32,914,946 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1132,850,902 - 32,914,464 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660691,957,798 - 2,024,004 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Syt10
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247782,700,545 - 2,763,134 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Syt10
350 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:12
Count of miRNA genes:12
Interacting mature miRNAs:12
Transcripts:ENSRNOT00000019406
Prediction methods:Miranda, Rnahybrid
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
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1582240Sffal1Serum free fatty acids level QTL 13.40.0021blood free fatty acid amount (VT:0001553)serum free fatty acids level (CMO:0000547)7116677010124049952Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)7116677189127103496Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

Markers in Region
D7Got235  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07130,786,157 - 130,786,399NCBIRnor6.0
Rnor_5.07130,469,515 - 130,469,757UniSTSRnor5.0
RGSC_v3.47128,132,749 - 128,132,991UniSTSRGSC3.4
Celera7117,351,660 - 117,351,902UniSTS
Cytogenetic Map7q34UniSTS


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 3
Low 63 10 16
Below cutoff 1 2 12 8 4 8 3 3 8 18 20 4 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019406   ⟹   ENSRNOP00000019406
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7120,864,997 - 120,920,863 (-)Ensembl
Rnor_6.0 Ensembl7130,768,841 - 130,827,152 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098923   ⟹   ENSRNOP00000091005
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7120,862,972 - 120,920,863 (-)Ensembl
RefSeq Acc Id: NM_031666   ⟹   NP_113854
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87122,737,301 - 122,800,462 (-)NCBI
mRatBN7.27120,857,698 - 120,920,863 (-)NCBI
Rnor_6.07130,769,039 - 130,827,030 (-)NCBI
Rnor_5.07130,452,003 - 130,510,388 (-)NCBI
RGSC_v3.47128,115,443 - 128,174,355 (-)RGD
Celera7117,334,018 - 117,391,703 (-)RGD
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_113854   ⟸   NM_031666
- UniProtKB: Q925B8 (UniProtKB/Swiss-Prot),   O08625 (UniProtKB/Swiss-Prot),   A6K7P3 (UniProtKB/TrEMBL),   Q1W5B9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019406   ⟸   ENSRNOT00000019406
RefSeq Acc Id: ENSRNOP00000091005   ⟸   ENSRNOT00000098923
Protein Domains
C2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O08625-F1-model_v2 AlphaFold O08625 1-523 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:62041 AgrOrtholog
BioCyc Gene G2FUF-32417 BioCyc
Ensembl Genes ENSRNOG00000014296 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055012196 UniProtKB/Swiss-Prot
  ENSRNOG00060025239 UniProtKB/Swiss-Prot
  ENSRNOG00065017388 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000019406.4 UniProtKB/TrEMBL
  ENSRNOT00000098923 ENTREZGENE
  ENSRNOT00000098923.1 UniProtKB/Swiss-Prot
  ENSRNOT00055020742 UniProtKB/Swiss-Prot
  ENSRNOT00060043735 UniProtKB/Swiss-Prot
  ENSRNOT00065029030 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:60567 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 60567 ENTREZGENE
PANTHER PTHR10024:SF46 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYNAPTOTAGMIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PF00168 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Syt10 PhenoGen
PRINTS C2DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYNAPTOTAGMN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PS50004 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000014296 RatGTEx
  ENSRNOG00055012196 RatGTEx
  ENSRNOG00060025239 RatGTEx
  ENSRNOG00065017388 RatGTEx
SMART SM00239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49562 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2QAR7_RAT UniProtKB/TrEMBL
  A6K7P3 ENTREZGENE, UniProtKB/TrEMBL
  O08625 ENTREZGENE
  Q1W5B9 ENTREZGENE, UniProtKB/TrEMBL
  Q925B8 ENTREZGENE
  SYT10_RAT UniProtKB/Swiss-Prot
UniProt Secondary Q925B8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Syt10  synaptotagmin 10  Syt10  synaptotagmin X  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Syt10  synaptotagmin X    synaptotagmin 10  Name updated 1299863 APPROVED
2002-06-10 Syt10  synaptotagmin 10      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_regulation expression induces in degenerating hippocampus and piriform cortex following kainic acid-induced seizure activity 61761