Syt15 (synaptotagmin 15) - Rat Genome Database

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Gene: Syt15 (synaptotagmin 15) Rattus norvegicus
Analyze
Symbol: Syt15
Name: synaptotagmin 15
RGD ID: 727964
Description: Predicted to enable SNARE binding activity; calcium ion sensor activity; and calcium-dependent phospholipid binding activity. Predicted to be involved in regulation of calcium ion-dependent exocytosis and vesicle-mediated transport. Predicted to be located in membrane. Predicted to be active in exocytic vesicle and plasma membrane. Orthologous to human SYT15 (synaptotagmin 15) and SYT15B (synaptotagmin 15B); 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 Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8169,538,740 - 9,549,548 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl169,538,748 - 9,549,558 (+)EnsemblGRCr8
mRatBN7.2169,532,478 - 9,543,288 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl169,532,478 - 9,543,281 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx169,545,819 - 9,556,742 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01610,690,525 - 10,701,447 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0169,540,888 - 9,551,812 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01610,554,136 - 10,564,934 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1610,554,136 - 10,564,927 (+)Ensemblrn6Rnor6.0
Rnor_5.0168,872,728 - 8,883,556 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4169,852,031 - 9,862,839 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera165,673,010 - 5,683,858 (-)NCBICelera
RGSC_v3.1169,852,028 - 9,862,835 (+)NCBI
Cytogenetic Map16p15NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl169,538,748 - 9,549,558 (+)EnsemblGRCr8
mRatBN7.2169,532,478 - 9,543,288 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl169,532,478 - 9,543,281 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx169,545,819 - 9,556,742 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01610,690,525 - 10,701,447 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0169,540,888 - 9,551,812 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01610,554,136 - 10,564,934 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1610,554,136 - 10,564,927 (+)Ensemblrn6Rnor6.0
Rnor_5.0168,872,728 - 8,883,556 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4169,852,031 - 9,862,839 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera165,673,010 - 5,683,858 (-)NCBICelera
RGSC_v3.1169,852,028 - 9,862,835 (+)NCBI
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 (+)Ensemblhg38GRCh38
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 EnsemblGRCm39
GRCm381434,219,956 - 34,230,421 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1434,219,595 - 34,230,420 (+)Ensemblmm10GRCm38
MGSCv371435,033,232 - 35,043,607 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
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_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0435,115,571 - 35,123,322 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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
SpeTri2.0 EnsemblNW_0049366015,293,681 - 5,300,131 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366015,292,516 - 5,301,871 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0

Variants

.
Variants in Syt15
67 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16423421216278352Rat
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1638712345387123Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133425095Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139568015Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16423421253708481Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16474422249744222Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16423421216278352Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16126734272Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126734272Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16435482249354822Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)1638712345387123Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16423421249757901Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16423421266955197Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16423421216061395Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139568015Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683908666195506Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338679049757901Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338679026128267Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683908666195506Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683908666195506Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126734272Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16423433317730812Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683908652786090Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683908666195506Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16330168348301683Rat

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

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
16 12 65 143 91 90 59 82 59 6 340 180 11 117 77 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000079030   ⟹   ENSRNOP00000075561
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl169,538,748 - 9,549,558 (+)Ensembl
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:
Protein Sequences
Protein RefSeqs NP_853663 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH84685 (Get FASTA)   NCBI Sequence Viewer  
  BAC76816 (Get FASTA)   NCBI Sequence Viewer  
  EDL88884 (Get FASTA)   NCBI Sequence Viewer  
  EDL88885 (Get FASTA)   NCBI Sequence Viewer  
  EDL88886 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000075561
GenBank Protein P59926 (Get FASTA)   NCBI Sequence Viewer  
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:
Ensembl 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
Ensembl Transcript ENSRNOT00000079030 ENTREZGENE
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7100793 IMAGE-MGC_LOAD
InterPro C2_dom UniProtKB/Swiss-Prot
  C2_domain_sf UniProtKB/Swiss-Prot
  Synaptotagmin-15/17_C2A UniProtKB/Swiss-Prot
MGC_CLONE MGC:91393 IMAGE-MGC_LOAD
NCBI Gene 306285 ENTREZGENE
PANTHER PTHR10024:SF234 UniProtKB/Swiss-Prot
  SYNAPTOTAGMIN UniProtKB/Swiss-Prot
Pfam PF00168 UniProtKB/Swiss-Prot
PhenoGen Syt15 PhenoGen
PROSITE PS50004 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000051688 RatGTEx
SMART SM00239 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49562 UniProtKB/Swiss-Prot
UniProt A0A0G2KAX3 ENTREZGENE, UniProtKB/TrEMBL
  A0ABZ3NNA4_RAT 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


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