Sytl4 (synaptotagmin-like 4) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Sytl4 (synaptotagmin-like 4) Rattus norvegicus
Analyze
Symbol: Sytl4
Name: synaptotagmin-like 4
RGD ID: 620204
Description: Predicted to enable neurexin family protein binding activity and phospholipid binding activity. Predicted to be involved in several processes, including plasma membrane repair; positive regulation of secretion by cell; and regulation of plasma membrane repair. Predicted to act upstream of or within negative regulation of insulin secretion. Located in apical plasma membrane. Orthologous to human SYTL4 (synaptotagmin like 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: exophilin-2; granuphilin b; synaptotagmin-like 4 (granuphilin-a); synaptotagmin-like protein 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X101,428,785 - 101,479,207 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX101,428,785 - 101,479,151 (-)EnsemblGRCr8
mRatBN7.2X97,135,496 - 97,185,867 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX97,135,500 - 97,185,854 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX98,811,171 - 98,836,894 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X102,320,957 - 102,346,675 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X99,824,353 - 99,850,072 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X104,763,961 - 104,814,152 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX104,765,294 - 104,814,145 (-)Ensemblrn6Rnor6.0
Rnor_5.0X104,598,207 - 104,648,029 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X121,473,414 - 121,499,134 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX98,183,387 - 98,209,107 (-)NCBICelera
RGSC_v3.1X121,546,846 - 121,572,567 (-)NCBI
Cytogenetic MapXq32NCBI
JBrowse:




Gene-Chemical Interaction 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. Pancreatic beta-cell protein granuphilin binds Rab3 and Munc-18 and controls exocytosis. Coppola T, etal., Mol Biol Cell 2002 Jun;13(6):1906-15.
2. Slp4-a/granuphilin-a regulates dense-core vesicle exocytosis in PC12 cells. Fukuda M, etal., J Biol Chem 2002 Oct 18;277(42):39673-8.
3. 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.
4. The small GTPase Rab27B regulates amylase release from rat parotid acinar cells. Imai A, etal., J Cell Sci. 2004 Apr 15;117(Pt 10):1945-53. Epub 2004 Mar 23.
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:2732579   PMID:10497219   PMID:11243866   PMID:12590134   PMID:16186111   PMID:16890542   PMID:18573236   PMID:19082571   PMID:19966785   PMID:22206666   PMID:25002582   PMID:27325790  


Genomics

Comparative Map Data
Sytl4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X101,428,785 - 101,479,207 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX101,428,785 - 101,479,151 (-)EnsemblGRCr8
mRatBN7.2X97,135,496 - 97,185,867 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX97,135,500 - 97,185,854 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX98,811,171 - 98,836,894 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X102,320,957 - 102,346,675 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X99,824,353 - 99,850,072 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X104,763,961 - 104,814,152 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX104,765,294 - 104,814,145 (-)Ensemblrn6Rnor6.0
Rnor_5.0X104,598,207 - 104,648,029 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X121,473,414 - 121,499,134 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX98,183,387 - 98,209,107 (-)NCBICelera
RGSC_v3.1X121,546,846 - 121,572,567 (-)NCBI
Cytogenetic MapXq32NCBI
SYTL4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X100,674,491 - 100,732,121 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX100,671,783 - 100,732,151 (-)Ensemblhg38GRCh38
GRCh37X99,929,488 - 99,987,108 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X99,816,144 - 99,873,154 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34X99,735,633 - 99,792,643NCBI
CeleraX100,448,228 - 100,505,895 (-)NCBICelera
Cytogenetic MapXq22.1NCBI
HuRefX89,729,520 - 89,785,468 (-)NCBIHuRef
CHM1_1X99,822,386 - 99,880,040 (-)NCBICHM1_1
T2T-CHM13v2.0X99,116,950 - 99,174,573 (-)NCBIT2T-CHM13v2.0
Sytl4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X132,837,134 - 132,882,569 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX132,837,134 - 132,882,561 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X133,936,385 - 133,981,821 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX133,936,385 - 133,981,812 (-)Ensemblmm10GRCm38
MGSCv37X130,470,924 - 130,516,322 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X129,282,735 - 129,328,133 (-)NCBIMGSCv36mm8
CeleraX116,812,358 - 116,857,700 (-)NCBICelera
Cytogenetic MapXE3NCBI
cM MapX55.47NCBI
Sytl4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555036,821,236 - 6,899,983 (-)Ensembl
ChiLan1.0NW_0049555036,821,263 - 6,899,983 (-)NCBIChiLan1.0ChiLan1.0
SYTL4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X100,279,112 - 100,338,151 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X100,285,847 - 100,341,747 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X89,885,478 - 89,941,381 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X100,024,434 - 100,051,663 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX100,024,434 - 100,051,663 (-)EnsemblpanPan2panpan1.1
SYTL4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X74,537,937 - 74,617,580 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX74,539,183 - 74,565,753 (-)EnsemblcanFam3CanFam3.1
ROS_Cfam_1.0X75,947,618 - 76,027,046 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX75,946,000 - 76,027,014 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X73,510,069 - 73,589,479 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X75,180,356 - 75,259,782 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X74,941,410 - 75,020,845 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Sytl4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X63,607,383 - 63,670,296 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365845,884,193 - 5,917,300 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365845,882,428 - 5,945,514 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYTL4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX82,367,549 - 82,437,401 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X82,367,546 - 82,437,439 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X90,208,955 - 90,310,119 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYTL4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X88,985,495 - 89,041,256 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX88,987,016 - 89,041,194 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606513,915,106 - 13,971,164 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sytl4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249021,876,516 - 1,942,265 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046249021,876,608 - 1,945,728 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Sytl4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X86,255,478 - 86,304,362 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sytl4
103 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:158
Count of miRNA genes:123
Interacting mature miRNAs:138
Transcripts:ENSRNOT00000004909, ENSRNOT00000004921
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, 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
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X97528096142528096Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X80434318125434318Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX92979612117740458Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
2302047Pia34Pristane induced arthritis QTL 345.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1996916163141916163Rat


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 67 153 91 90 59 81 59 6 345 181 11 132 81 92 31 11 11

Sequence


Ensembl Acc Id: ENSRNOT00000004909   ⟹   ENSRNOP00000004909
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX101,439,453 - 101,479,151 (-)Ensembl
mRatBN7.2 EnsemblX97,146,164 - 97,185,854 (-)Ensembl
Rnor_6.0 EnsemblX104,765,294 - 104,814,145 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000004921   ⟹   ENSRNOP00000004921
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX101,430,320 - 101,479,151 (-)Ensembl
mRatBN7.2 EnsemblX97,137,031 - 97,185,854 (-)Ensembl
Rnor_6.0 EnsemblX104,765,492 - 104,791,210 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000113853   ⟹   ENSRNOP00000078420
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX101,428,785 - 101,479,151 (-)Ensembl
mRatBN7.2 EnsemblX97,135,500 - 97,185,854 (-)Ensembl
RefSeq Acc Id: NM_080410   ⟹   NP_536335
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,428,785 - 101,479,151 (-)NCBI
mRatBN7.2X97,135,496 - 97,185,866 (-)NCBI
Rnor_6.0X104,765,492 - 104,791,210 (-)NCBI
Rnor_5.0X104,598,207 - 104,648,029 (-)NCBI
RGSC_v3.4X121,473,414 - 121,499,134 (-)RGD
CeleraX98,183,387 - 98,209,107 (-)RGD
Sequence:
RefSeq Acc Id: XM_008773387   ⟹   XP_008771609
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,428,791 - 101,479,207 (-)NCBI
mRatBN7.2X97,135,500 - 97,185,867 (-)NCBI
Rnor_6.0X104,765,486 - 104,814,151 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099429   ⟹   XP_038955357
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,428,791 - 101,479,109 (-)NCBI
mRatBN7.2X97,135,500 - 97,185,867 (-)NCBI
RefSeq Acc Id: XM_039099431   ⟹   XP_038955359
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,428,791 - 101,479,151 (-)NCBI
mRatBN7.2X97,135,500 - 97,185,865 (-)NCBI
RefSeq Acc Id: XM_063279762   ⟹   XP_063135832
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,428,791 - 101,479,109 (-)NCBI
RefSeq Acc Id: XM_063279763   ⟹   XP_063135833
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,428,791 - 101,479,151 (-)NCBI
RefSeq Acc Id: NP_536335   ⟸   NM_080410
- UniProtKB: Q8VHQ7 (UniProtKB/Swiss-Prot),   Q8VHQ6 (UniProtKB/Swiss-Prot),   A0A8I5ZMC6 (UniProtKB/TrEMBL),   A6IVE0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771609   ⟸   XM_008773387
- Peptide Label: isoform X2
- UniProtKB: D3ZTZ2 (UniProtKB/TrEMBL),   A6IVE1 (UniProtKB/TrEMBL),   G3V6G6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000004921   ⟸   ENSRNOT00000004921
Ensembl Acc Id: ENSRNOP00000004909   ⟸   ENSRNOT00000004909
RefSeq Acc Id: XP_038955357   ⟸   XM_039099429
- Peptide Label: isoform X1
- UniProtKB: Q8VHQ7 (UniProtKB/Swiss-Prot),   Q8VHQ6 (UniProtKB/Swiss-Prot),   A0A8I5ZMC6 (UniProtKB/TrEMBL),   A6IVE0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955359   ⟸   XM_039099431
- Peptide Label: isoform X1
- UniProtKB: Q8VHQ7 (UniProtKB/Swiss-Prot),   Q8VHQ6 (UniProtKB/Swiss-Prot),   A0A8I5ZMC6 (UniProtKB/TrEMBL),   A6IVE0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000078420   ⟸   ENSRNOT00000113853
RefSeq Acc Id: XP_063135833   ⟸   XM_063279763
- Peptide Label: isoform X2
- UniProtKB: G3V6G6 (UniProtKB/TrEMBL),   A6IVE1 (UniProtKB/TrEMBL),   D3ZTZ2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135832   ⟸   XM_063279762
- Peptide Label: isoform X2
- UniProtKB: G3V6G6 (UniProtKB/TrEMBL),   A6IVE1 (UniProtKB/TrEMBL),   D3ZTZ2 (UniProtKB/TrEMBL)
Protein Domains
C2   RabBD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8VHQ7-F1-model_v2 AlphaFold Q8VHQ7 1-672 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:620204 AgrOrtholog
BIND 134440
  134444
  134445
  134446
BioCyc Gene G2FUF-1697 BioCyc
Ensembl Genes ENSRNOG00000003526 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000004921 ENTREZGENE
  ENSRNOT00000113853 ENTREZGENE
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot
  3.30.40.10 UniProtKB/Swiss-Prot
InterPro C2_dom UniProtKB/Swiss-Prot
  C2_domain_sf UniProtKB/Swiss-Prot
  FYVE_2 UniProtKB/Swiss-Prot
  FYVE_Slp4 UniProtKB/Swiss-Prot
  Rab_BD UniProtKB/Swiss-Prot
  SLP-4/5_C2A UniProtKB/Swiss-Prot
  SYTL1-5_C2B UniProtKB/Swiss-Prot
  Znf_FYVE_PHD UniProtKB/Swiss-Prot
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot
KEGG Report rno:140594 UniProtKB/Swiss-Prot
NCBI Gene 140594 ENTREZGENE
PANTHER BITESIZE, ISOFORM I UniProtKB/Swiss-Prot
  PTHR45716:SF4 UniProtKB/Swiss-Prot
Pfam FYVE_2 UniProtKB/Swiss-Prot
  PF00168 UniProtKB/Swiss-Prot
PhenoGen Sytl4 PhenoGen
PROSITE PS50004 UniProtKB/Swiss-Prot
  RABBD UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000003526 RatGTEx
SMART SM00239 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49562 UniProtKB/Swiss-Prot
  SSF57903 UniProtKB/Swiss-Prot
UniProt A0A8I5ZMC6 ENTREZGENE, UniProtKB/TrEMBL
  A6IVE0 ENTREZGENE, UniProtKB/TrEMBL
  A6IVE1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZTZ2 ENTREZGENE, UniProtKB/TrEMBL
  G3V6G6 ENTREZGENE, UniProtKB/TrEMBL
  Q8VHQ6 ENTREZGENE
  Q8VHQ7 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q8VHQ6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-07-08 Sytl4  synaptotagmin-like 4    synaptotagmin-like 4 (granuphilin-a)  Name updated 1299863 APPROVED
2002-08-07 Sytl4  synaptotagmin-like 4 (granuphilin-a)      Symbol and Name status set to provisional 70820 PROVISIONAL