Syde2 (synapse defective Rho GTPase homolog 2) - Rat Genome Database

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Gene: Syde2 (synapse defective Rho GTPase homolog 2) Rattus norvegicus
Analyze
Symbol: Syde2
Name: synapse defective Rho GTPase homolog 2
RGD ID: 1564206
Description: Predicted to enable GTPase activator activity. Predicted to be involved in cell migration and regulation of Ras protein signal transduction. Predicted to be active in synaptic membrane. Orthologous to human SYDE2 (synapse defective Rho GTPase homolog 2); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC308021; RGD1564206; rho GTPase-activating protein SYDE2; similar to hypothetical protein FLJ13511; Syde2-ps1; synapse defective 1, Rho GTPase, homolog 2; synapse defective 1, Rho GTPase, homolog 2 (C. elegans); synapse defective 1, Rho GTPase, homolog 2 (C. elegans), pseudogene 1; synapse defective 1, Rho GTPase, homolog 2, pseudogene 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82237,557,395 - 237,591,290 (+)NCBIGRCr8
mRatBN7.22234,897,975 - 234,930,994 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2234,897,717 - 234,930,994 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2242,690,164 - 242,723,132 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02240,580,564 - 240,613,520 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02235,447,782 - 235,480,755 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02251,861,900 - 251,895,524 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2251,863,069 - 251,894,037 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02270,385,411 - 270,419,064 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42244,166,412 - 244,199,033 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2226,880,380 - 226,913,328 (+)NCBICelera
Cytogenetic Map2q44NCBI
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

Biological Process

Cellular Component

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:27917469  


Genomics

Comparative Map Data
Syde2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82237,557,395 - 237,591,290 (+)NCBIGRCr8
mRatBN7.22234,897,975 - 234,930,994 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2234,897,717 - 234,930,994 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2242,690,164 - 242,723,132 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02240,580,564 - 240,613,520 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02235,447,782 - 235,480,755 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02251,861,900 - 251,895,524 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2251,863,069 - 251,894,037 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02270,385,411 - 270,419,064 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42244,166,412 - 244,199,033 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2226,880,380 - 226,913,328 (+)NCBICelera
Cytogenetic Map2q44NCBI
SYDE2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38185,152,491 - 85,201,016 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl185,156,889 - 85,201,724 (-)EnsemblGRCh38hg38GRCh38
GRCh37185,622,572 - 85,666,699 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36185,395,944 - 85,439,316 (-)NCBINCBI36Build 36hg18NCBI36
Celera183,867,794 - 83,911,153 (-)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef183,733,947 - 83,777,560 (-)NCBIHuRef
CHM1_1185,738,965 - 85,782,326 (-)NCBICHM1_1
T2T-CHM13v2.0184,997,997 - 85,042,131 (-)NCBIT2T-CHM13v2.0
Syde2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393145,693,160 - 145,727,475 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3145,693,625 - 145,727,475 (+)EnsemblGRCm39 Ensembl
GRCm383145,987,405 - 146,021,720 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3145,987,870 - 146,021,720 (+)EnsemblGRCm38mm10GRCm38
MGSCv373145,650,834 - 145,684,684 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363145,924,785 - 145,959,489 (+)NCBIMGSCv36mm8
MGSCv363146,523,395 - 146,558,245 (+)NCBIMGSCv36mm8
Celera3152,441,267 - 152,475,540 (+)NCBICelera
Cytogenetic Map3H2NCBI
cM Map371.03NCBI
Syde2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554238,783,116 - 8,838,665 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554238,783,116 - 8,839,927 (+)NCBIChiLan1.0ChiLan1.0
SYDE2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21141,731,421 - 141,781,181 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11140,886,701 - 140,936,510 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01117,713,925 - 117,759,382 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1186,571,404 - 86,615,051 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl186,571,431 - 86,615,051 (-)Ensemblpanpan1.1panPan2
SYDE2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1662,768,892 - 62,822,550 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl662,775,056 - 62,820,677 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha665,422,892 - 65,471,269 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0663,314,310 - 63,362,687 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl663,314,148 - 63,360,988 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1662,841,461 - 62,889,829 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0662,811,662 - 62,860,036 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0663,319,495 - 63,367,884 (+)NCBIUU_Cfam_GSD_1.0
Syde2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505895,765,663 - 95,803,177 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936608503,043 - 540,359 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936608502,909 - 540,370 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYDE2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4130,702,424 - 130,749,734 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14130,702,340 - 130,749,742 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24143,278,477 - 143,325,873 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYDE2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12048,146,793 - 48,190,946 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2048,149,023 - 48,190,190 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603369,618,409 - 69,660,914 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Syde2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474212,299,316 - 12,344,180 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474212,299,250 - 12,349,945 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Syde2
225 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:115
Count of miRNA genes:97
Interacting mature miRNAs:104
Transcripts:ENSRNOT00000036282
Prediction methods:Microtar, Miranda, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2200990457245990457Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2202446871237938339Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2211744537249053267Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2211744537249053267Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2211744537249053267Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2211744537249053267Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2211744537249053267Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2212828222249053267Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2214226044247136170Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2215377404237938339Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2218414747240841241Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2223389739249053267Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2223389739249053267Rat
631563Hcuc3Hepatic copper content QTL 33.87liver copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2229059610249053267Rat

Markers in Region
AI408386  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22234,930,561 - 234,930,790 (+)MAPPERmRatBN7.2
Rnor_6.02251,895,092 - 251,895,320NCBIRnor6.0
Rnor_5.02270,418,632 - 270,418,860UniSTSRnor5.0
RGSC_v3.42244,200,088 - 244,200,316UniSTSRGSC3.4
Celera2226,912,896 - 226,913,124UniSTS
Cytogenetic Map2q44UniSTS


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 1 3 2 2 2 26 22 11
Low 2 43 54 39 19 39 8 9 72 9 17 8
Below cutoff 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000036282   ⟹   ENSRNOP00000031789
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2234,897,717 - 234,930,994 (+)Ensembl
Rnor_6.0 Ensembl2251,863,069 - 251,894,037 (+)Ensembl
RefSeq Acc Id: NM_001305229   ⟹   NP_001292158
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82237,558,274 - 237,591,290 (+)NCBI
mRatBN7.22234,897,975 - 234,930,994 (+)NCBI
Rnor_6.02251,862,473 - 251,895,524 (+)NCBI
Celera2226,880,380 - 226,913,328 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590812   ⟹   XP_017446301
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82237,557,395 - 237,591,282 (+)NCBI
mRatBN7.22234,898,001 - 234,930,986 (+)NCBI
Rnor_6.02251,861,901 - 251,895,524 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590814   ⟹   XP_017446303
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82237,557,395 - 237,589,444 (+)NCBI
mRatBN7.22234,897,998 - 234,929,148 (+)NCBI
Rnor_6.02251,861,900 - 251,893,626 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039102135   ⟹   XP_038958063
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82237,557,395 - 237,591,282 (+)NCBI
mRatBN7.22234,898,000 - 234,930,986 (+)NCBI
RefSeq Acc Id: XM_039102136   ⟹   XP_038958064
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82237,557,395 - 237,591,282 (+)NCBI
mRatBN7.22234,897,997 - 234,929,154 (+)NCBI
RefSeq Acc Id: XM_039102137   ⟹   XP_038958065
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82237,557,395 - 237,589,443 (+)NCBI
mRatBN7.22234,897,997 - 234,929,145 (+)NCBI
RefSeq Acc Id: XM_063281682   ⟹   XP_063137752
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82237,557,395 - 237,591,282 (+)NCBI
RefSeq Acc Id: XR_005500274
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82237,557,395 - 237,589,329 (+)NCBI
mRatBN7.22234,897,998 - 234,929,027 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001292158   ⟸   NM_001305229
- UniProtKB: A6HWC8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017446303   ⟸   XM_017590814
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017446301   ⟸   XM_017590812
- Peptide Label: isoform X1
- UniProtKB: F1LVD8 (UniProtKB/TrEMBL),   A6HWC8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000031789   ⟸   ENSRNOT00000036282
RefSeq Acc Id: XP_038958064   ⟸   XM_039102136
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038958065   ⟸   XM_039102137
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038958063   ⟸   XM_039102135
- Peptide Label: isoform X2
- UniProtKB: A6HWC8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063137752   ⟸   XM_063281682
- Peptide Label: isoform X4
Protein Domains
C2   Rho-GAP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LVD8-F1-model_v2 AlphaFold F1LVD8 1-1171 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:1564206 AgrOrtholog
BioCyc Gene G2FUF-50910 BioCyc
Ensembl Genes ENSRNOG00000026186 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000036282.7 UniProtKB/TrEMBL
Gene3D-CATH 1.10.555.10 UniProtKB/TrEMBL
  2.60.40.150 UniProtKB/TrEMBL
InterPro C2_dom UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/TrEMBL
  Rho_GTPase_activation_prot UniProtKB/TrEMBL
  RhoGAP_dom UniProtKB/TrEMBL
NCBI Gene 308021 ENTREZGENE
PANTHER RHO GTPASE-ACTIVATING PROTEIN 100F UniProtKB/TrEMBL
  RHO GTPASE-ACTIVATING PROTEIN SYDE2 UniProtKB/TrEMBL
Pfam RhoGAP UniProtKB/TrEMBL
PhenoGen Syde2 PhenoGen
PROSITE PS50004 UniProtKB/TrEMBL
  RHOGAP UniProtKB/TrEMBL
RatGTEx ENSRNOG00000026186 RatGTEx
SMART RhoGAP UniProtKB/TrEMBL
Superfamily-SCOP Rho_GAP UniProtKB/TrEMBL
  SSF49562 UniProtKB/TrEMBL
UniProt A6HWC8 ENTREZGENE, UniProtKB/TrEMBL
  F1LVD8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-05 Syde2  synapse defective Rho GTPase homolog 2  Syde2  synapse defective 1, Rho GTPase, homolog 2 (C. elegans)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-03-07 Syde2  synapse defective 1, Rho GTPase, homolog 2 (C. elegans)  Syde2-ps1  synapse defective 1, Rho GTPase, homolog 2 (C. elegans), pseudogene 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-06-09 Syde2-ps1  synapse defective 1, Rho GTPase, homolog 2 (C. elegans), pseudogene 1  Syde2  synapse defective 1, Rho GTPase, homolog 2 (C. elegans)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Syde2  synapse defective 1, Rho GTPase, homolog 2 (C. elegans)  RGD1564206_predicted  similar to hypothetical protein FLJ13511 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564206_predicted  similar to hypothetical protein FLJ13511 (predicted)  LOC308021  similar to hypothetical protein FLJ13511  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC308021  similar to hypothetical protein FLJ13511      Symbol and Name status set to provisional 70820 PROVISIONAL