Esyt3 (extended synaptotagmin 3) - Rat Genome Database

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Gene: Esyt3 (extended synaptotagmin 3) Rattus norvegicus
Analyze
Symbol: Esyt3
Name: extended synaptotagmin 3
RGD ID: 1561304
Description: Predicted to enable calcium ion binding activity and phospholipid binding activity. Predicted to be involved in endoplasmic reticulum-plasma membrane tethering and lipid transport. Predicted to be located in cytoplasmic side of plasma membrane and endoplasmic reticulum-plasma membrane contact site. Predicted to be active in endoplasmic reticulum membrane. Orthologous to human ESYT3 (extended synaptotagmin 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; alpha-Zearalanol; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: extended synaptotagmin protein 3; extended synaptotagmin-3; extended synaptotagmin-like protein 3; Fam62c; family with sequence similarity 62 (C2 domain containing), member C; LOC363120; RGD1561304; similar to hypothetical protein D930024E11
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
GRCr88108,749,761 - 108,796,630 (-)NCBIGRCr8
mRatBN7.2899,870,418 - 99,917,298 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl899,871,149 - 99,917,232 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.08107,555,417 - 107,602,414 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8107,555,277 - 107,602,263 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08106,981,121 - 107,027,963 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48104,171,726 - 104,216,761 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera899,272,485 - 99,319,481 (-)NCBICelera
Cytogenetic Map8q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17360437   PMID:23791178   PMID:30220461  


Genomics

Comparative Map Data
Esyt3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88108,749,761 - 108,796,630 (-)NCBIGRCr8
mRatBN7.2899,870,418 - 99,917,298 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl899,871,149 - 99,917,232 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.08107,555,417 - 107,602,414 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8107,555,277 - 107,602,263 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08106,981,121 - 107,027,963 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48104,171,726 - 104,216,761 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera899,272,485 - 99,319,481 (-)NCBICelera
Cytogenetic Map8q31NCBI
ESYT3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383138,434,616 - 138,481,686 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3138,434,586 - 138,481,686 (+)EnsemblGRCh38hg38GRCh38
GRCh373138,153,458 - 138,200,528 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363139,636,109 - 139,678,399 (+)NCBINCBI36Build 36hg18NCBI36
Celera3136,578,324 - 136,622,170 (+)NCBICelera
Cytogenetic Map3q22.3NCBI
HuRef3135,528,375 - 135,572,226 (+)NCBIHuRef
CHM1_13138,117,188 - 138,161,034 (+)NCBICHM1_1
T2T-CHM13v2.03141,175,169 - 141,222,247 (+)NCBIT2T-CHM13v2.0
Esyt3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39999,192,016 - 99,242,210 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl999,192,016 - 99,240,610 (-)EnsemblGRCm39 Ensembl
GRCm38999,309,963 - 99,360,159 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl999,309,963 - 99,358,557 (-)EnsemblGRCm38mm10GRCm38
MGSCv37999,210,386 - 99,258,949 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36999,119,495 - 99,167,882 (-)NCBIMGSCv36mm8
Celera998,843,495 - 98,893,869 (-)NCBICelera
Cytogenetic Map9E3.3NCBI
cM Map951.54NCBI
Esyt3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955501538,538 - 585,505 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955501537,195 - 585,640 (-)NCBIChiLan1.0ChiLan1.0
ESYT3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22136,340,722 - 136,384,571 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13136,345,050 - 136,392,918 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03135,463,698 - 135,509,417 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13142,913,450 - 142,958,684 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3142,913,450 - 142,958,684 (+)Ensemblpanpan1.1panPan2
ESYT3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12334,645,248 - 34,692,178 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2334,645,087 - 34,691,939 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2334,639,173 - 34,685,862 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02335,187,397 - 35,234,172 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2335,187,162 - 35,233,932 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12334,868,467 - 34,915,155 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02334,934,284 - 34,980,995 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02335,185,169 - 35,231,861 (+)NCBIUU_Cfam_GSD_1.0
Esyt3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560274,005,161 - 74,046,610 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936540744,980 - 785,113 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936540744,980 - 786,303 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ESYT3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1379,245,836 - 79,297,334 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11379,245,818 - 79,295,471 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21386,861,629 - 86,898,873 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ESYT3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11552,062,156 - 52,130,942 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1552,062,357 - 52,104,852 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604125,074,492 - 25,119,220 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Esyt3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473014,986,750 - 15,033,870 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473014,986,583 - 15,035,163 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Esyt3
200 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:333
Count of miRNA genes:201
Interacting mature miRNAs:239
Transcripts:ENSRNOT00000017658
Prediction methods:Microtar, 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
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)854259986100382532Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
8693654Alc32Alcohol consumption QTL 3220.755drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)888612425107550209Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
1578755Pur5Proteinuria QTL 53.30.0001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)889265192114019816Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088626Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat

Markers in Region
AW532330  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2899,870,448 - 99,870,629 (+)MAPPERmRatBN7.2
Rnor_6.08107,555,444 - 107,555,624NCBIRnor6.0
Rnor_5.08106,981,148 - 106,981,328UniSTSRnor5.0
RGSC_v3.48104,170,113 - 104,170,293UniSTSRGSC3.4
Celera899,272,512 - 99,272,692UniSTS
RH 3.4 Map81039.59UniSTS
Cytogenetic Map8q31UniSTS
BM386519  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr88108,754,325 - 108,754,963 (+)Marker Load Pipeline
mRatBN7.2899,874,984 - 99,875,622 (+)MAPPERmRatBN7.2
Rnor_6.08107,559,980 - 107,560,617NCBIRnor6.0
Rnor_5.08106,985,684 - 106,986,321UniSTSRnor5.0
RGSC_v3.48104,174,649 - 104,175,286UniSTSRGSC3.4
Celera899,277,049 - 99,277,686UniSTS
RH 3.4 Map81038.79UniSTS
Cytogenetic Map8q31UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 8 46 111 82 81 50 25 50 6 203 92 91 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000017658   ⟹   ENSRNOP00000017658
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl899,871,149 - 99,917,232 (-)Ensembl
Rnor_6.0 Ensembl8107,555,277 - 107,602,263 (-)Ensembl
RefSeq Acc Id: XM_063266440   ⟹   XP_063122510
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88108,749,761 - 108,796,630 (-)NCBI
RefSeq Acc Id: XM_063266441   ⟹   XP_063122511
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88108,749,761 - 108,796,630 (-)NCBI
RefSeq Acc Id: XM_063266442   ⟹   XP_063122512
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88108,749,761 - 108,762,152 (-)NCBI
RefSeq Acc Id: XM_343454   ⟹   XP_343455
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88108,749,761 - 108,796,630 (-)NCBI
mRatBN7.2899,870,418 - 99,917,298 (-)NCBI
Rnor_6.08107,555,417 - 107,602,414 (-)NCBI
Rnor_5.08106,981,121 - 107,027,963 (-)NCBI
RGSC_v3.48104,171,726 - 104,216,761 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001416359 (Get FASTA)   NCBI Sequence Viewer  
  XP_063122510 (Get FASTA)   NCBI Sequence Viewer  
  XP_063122511 (Get FASTA)   NCBI Sequence Viewer  
  XP_063122512 (Get FASTA)   NCBI Sequence Viewer  
  XP_343455 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL77444 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000017658.6
RefSeq Acc Id: XP_343455   ⟸   XM_343454
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000017658   ⟸   ENSRNOT00000017658
RefSeq Acc Id: XP_063122511   ⟸   XM_063266441
- Peptide Label: isoform X3
- UniProtKB: A6I2D3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063122510   ⟸   XM_063266440
- Peptide Label: isoform X2
- UniProtKB: A6I2D3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063122512   ⟸   XM_063266442
- Peptide Label: isoform X4
Protein Domains
C2   SMP-LTD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZC04-F1-model_v2 AlphaFold D3ZC04 1-890 view protein structure

Transcriptome

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

Promoters
RGD ID:13696214
Promoter ID:EPDNEW_R6734
Type:multiple initiation site
Name:Esyt3_1
Description:extended synaptotagmin 3
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_6.08107,602,244 - 107,602,304EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561304 AgrOrtholog
BioCyc Gene G2FUF-29397 BioCyc
Ensembl Genes ENSRNOG00000022704 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017658.8 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.150 UniProtKB/TrEMBL
InterPro C2_Ca-dep UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/TrEMBL
  C2C_KIAA1228 UniProtKB/TrEMBL
  Ext_Synaptotagmin_C2A UniProtKB/TrEMBL
  Ext_Synaptotagmin_C2B UniProtKB/TrEMBL
  Extended_Synaptotagmin UniProtKB/TrEMBL
  SMP_LBD UniProtKB/TrEMBL
  Synaptotagmin_SMP UniProtKB/TrEMBL
KEGG Report rno:363120 UniProtKB/TrEMBL
NCBI Gene 363120 ENTREZGENE
PANTHER EXTENDED SYNAPTOTAGMIN-3 UniProtKB/TrEMBL
  EXTENDED SYNAPTOTAGMIN-LIKE PROTEIN 2, ISOFORM C UniProtKB/TrEMBL
Pfam PF00168 UniProtKB/TrEMBL
  SMP_LBD UniProtKB/TrEMBL
PhenoGen Esyt3 PhenoGen
PRINTS C2DOMAIN UniProtKB/TrEMBL
PROSITE PS50004 UniProtKB/TrEMBL
  SMP UniProtKB/TrEMBL
RatGTEx ENSRNOG00000022704 RatGTEx
SMART SM00239 UniProtKB/TrEMBL
Superfamily-SCOP SSF49562 UniProtKB/TrEMBL
UniProt A6I2D3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZC04 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-22 Esyt3  extended synaptotagmin 3  Esyt3  extended synaptotagmin protein 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-15 Esyt3  extended synaptotagmin protein 3  Esyt3  extended synaptotagmin-like protein 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-10-22 Esyt3  extended synaptotagmin-like protein 3  Fam62c  family with sequence similarity 62 (C2 domain containing), member C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Fam62c  family with sequence similarity 62 (C2 domain containing), member C  RGD1561304_predicted  similar to hypothetical protein D930024E11 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561304_predicted  similar to hypothetical protein D930024E11 (predicted)  LOC363120  similar to hypothetical protein D930024E11  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC363120  similar to hypothetical protein D930024E11      Symbol and Name status set to provisional 70820 PROVISIONAL