Syt15 (synaptotagmin 15) - Rat Genome Database

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Gene: Syt15 (synaptotagmin 15) Rattus norvegicus
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Symbol: Syt15
Name: synaptotagmin 15
RGD ID: 727964
Description: Predicted to enable several functions, including calcium ion binding activity; phospholipid binding activity; and syntaxin binding activity. Predicted to be involved in calcium-ion regulated exocytosis; cellular response to calcium ion; and regulation of secretion by cell. Predicted to be located in membrane. Predicted to be active in exocytic vesicle and plasma membrane. Orthologous to human SYT15 (synaptotagmin 15); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC91393; synaptotagmin XV; synaptotagmin-15; sytXV
RGD Orthologs
Human
Mouse
Dog
Squirrel
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8169,538,740 - 9,549,548 (+)NCBIGRCr8
mRatBN7.2169,532,478 - 9,543,288 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl169,532,478 - 9,543,281 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx169,545,819 - 9,556,742 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01610,690,525 - 10,701,447 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0169,540,888 - 9,551,812 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01610,554,136 - 10,564,934 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1610,554,136 - 10,564,927 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0168,872,728 - 8,883,556 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4169,852,031 - 9,862,839 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1169,852,028 - 9,862,835 (+)NCBI
Celera165,673,010 - 5,683,858 (-)NCBICelera
Cytogenetic Map16p15NCBI
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
exocytic vesicle  (IBA,IEA)
membrane  (IEA,ISO)
plasma membrane  (IBA,IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Molecular cloning and characterization of human, rat, and mouse synaptotagmin XV. Fukuda M Biochem Biophys Res Commun 2003 Jun 20;306(1):64-71.
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. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
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:12477932   PMID:12765241  


Genomics

Comparative Map Data
Syt15
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8169,538,740 - 9,549,548 (+)NCBIGRCr8
mRatBN7.2169,532,478 - 9,543,288 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl169,532,478 - 9,543,281 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx169,545,819 - 9,556,742 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01610,690,525 - 10,701,447 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0169,540,888 - 9,551,812 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01610,554,136 - 10,564,934 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1610,554,136 - 10,564,927 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0168,872,728 - 8,883,556 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4169,852,031 - 9,862,839 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1169,852,028 - 9,862,835 (+)NCBI
Celera165,673,010 - 5,683,858 (-)NCBICelera
Cytogenetic Map16p15NCBI
SYT15
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381046,579,128 - 46,597,108 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1046,578,217 - 46,594,173 (+)EnsemblGRCh38hg38GRCh38
GRCh371046,955,444 - 46,970,489 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map10q11.22NCBI
HuRef1042,812,620 - 42,814,634 (-)NCBIHuRef
HuRef1042,807,574 - 42,812,405 (-)NCBIHuRef
CHM1_11047,025,127 - 47,040,282 (-)NCBICHM1_1
T2T-CHM13v2.01047,465,488 - 47,482,877 (+)NCBIT2T-CHM13v2.0
Syt15
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391433,941,915 - 33,952,378 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1433,941,552 - 33,952,377 (+)EnsemblGRCm39 Ensembl
GRCm381434,219,956 - 34,230,421 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1434,219,595 - 34,230,420 (+)EnsemblGRCm38mm10GRCm38
MGSCv371435,033,232 - 35,043,607 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361433,049,139 - 33,059,513 (+)NCBIMGSCv36mm8
Celera1430,482,178 - 30,492,563 (+)NCBICelera
Cytogenetic Map14BNCBI
cM Map1420.8NCBI
LOC489080
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1434,754,250 - 34,763,273 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha434,746,235 - 34,754,762 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0435,115,571 - 35,123,322 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1434,960,443 - 34,969,012 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0435,129,569 - 35,138,128 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0435,636,053 - 35,644,631 (-)NCBIUU_Cfam_GSD_1.0
Syt15
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721343,659,628 - 43,669,465 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366015,292,516 - 5,301,871 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0

Variants

.
Variants in Syt15
82 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:290
Count of miRNA genes:192
Interacting mature miRNAs:237
Transcripts:ENSRNOT00000027475
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
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16285170915884239Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760916039848Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16422773017696785Rat

Markers in Region
AW534054  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2169,535,091 - 9,535,249 (+)MAPPERmRatBN7.2
Rnor_6.01610,556,738 - 10,556,895NCBIRnor6.0
Rnor_5.0168,875,360 - 8,875,517UniSTSRnor5.0
RGSC_v3.4169,854,643 - 9,854,800UniSTSRGSC3.4
Celera165,681,049 - 5,681,206UniSTS
RH 3.4 Map1691.5UniSTS
Cytogenetic Map16p16UniSTS


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
Low 3 2 22 13 18 13 2 2 19 32 31 11 2
Below cutoff 39 35 28 1 28 6 9 47 3 10 6

Sequence


RefSeq Acc Id: ENSRNOT00000079030   ⟹   ENSRNOP00000075561
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl169,532,478 - 9,543,281 (+)Ensembl
Rnor_6.0 Ensembl1610,554,136 - 10,564,927 (+)Ensembl
RefSeq Acc Id: NM_181632   ⟹   NP_853663
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,538,740 - 9,549,548 (+)NCBI
mRatBN7.2169,532,478 - 9,543,288 (+)NCBI
Rnor_6.01610,554,136 - 10,564,934 (+)NCBI
Rnor_5.0168,872,728 - 8,883,556 (+)NCBI
RGSC_v3.4169,852,031 - 9,862,839 (+)RGD
Celera165,673,010 - 5,683,858 (-)RGD
Sequence:
RefSeq Acc Id: NP_853663   ⟸   NM_181632
- UniProtKB: P59926 (UniProtKB/Swiss-Prot),   Q5XFY6 (UniProtKB/TrEMBL),   F1LQ33 (UniProtKB/TrEMBL),   A6KFS7 (UniProtKB/TrEMBL),   A0A0G2KAX3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075561   ⟸   ENSRNOT00000079030
Protein Domains
C2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P59926-F1-model_v2 AlphaFold P59926 1-422 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:727964 AgrOrtholog
BioCyc Gene G2FUF-12069 BioCyc
Ensembl Genes ENSRNOG00000051688 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00055010453 UniProtKB/Swiss-Prot
  ENSRNOG00060013201 UniProtKB/Swiss-Prot
  ENSRNOG00065014123 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000079030 ENTREZGENE
  ENSRNOT00000079030.2 UniProtKB/TrEMBL
  ENSRNOT00055017687 UniProtKB/Swiss-Prot
  ENSRNOT00060022499 UniProtKB/Swiss-Prot
  ENSRNOT00065023318 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7100793 IMAGE-MGC_LOAD
InterPro C2_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synaptotagmin-15/17_C2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:306285 UniProtKB/TrEMBL
MGC_CLONE MGC:91393 IMAGE-MGC_LOAD
NCBI Gene 306285 ENTREZGENE
PANTHER PTHR10024:SF234 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYNAPTOTAGMIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PF00168 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Syt15 PhenoGen
PROSITE PS50004 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000051688 RatGTEx
  ENSRNOG00055010453 RatGTEx
  ENSRNOG00060013201 RatGTEx
  ENSRNOG00065014123 RatGTEx
SMART SM00239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49562 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2KAX3 ENTREZGENE, UniProtKB/TrEMBL
  A6KFS7 ENTREZGENE, UniProtKB/TrEMBL
  A6KFS8_RAT UniProtKB/TrEMBL
  A6KFS9_RAT UniProtKB/TrEMBL
  F1LQ33 ENTREZGENE
  P59926 ENTREZGENE
  Q5XFY6 ENTREZGENE
  SYT15_RAT UniProtKB/Swiss-Prot
UniProt Secondary F1LQ33 UniProtKB/TrEMBL
  Q5XFY6 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Syt15  synaptotagmin 15  Syt15  synaptotagmin XV  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Syt15  synaptotagmin XV  Syt15  synaptotagmin 15  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Syt15  synaptotagmin 15  sytXV  synaptotagmin XV  Symbol and Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in mainly non-neuronal tissues 1299614