Syde1 (synapse defective Rho GTPase homolog 1) - Rat Genome Database

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Gene: Syde1 (synapse defective Rho GTPase homolog 1) Rattus norvegicus
Analyze
Symbol: Syde1
Name: synapse defective Rho GTPase homolog 1
RGD ID: 1305857
Description: Predicted to enable GTPase activator activity. Predicted to be involved in several processes, including positive regulation of trophoblast cell migration; regulation of Ras protein signal transduction; and regulation of cytoskeleton organization. Predicted to act upstream of or within several processes, including labyrinthine layer blood vessel development; synaptic vesicle docking; and synaptonemal complex assembly. Predicted to be located in cerebellar mossy fiber and cytosol. Predicted to be active in synaptic membrane. Orthologous to human SYDE1 (synapse defective Rho GTPase homolog 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC362842; RGD1305857; rho GTPase-activating protein SYDE1; similar to hypothetical protein FLJ13511; synapse defective 1, Rho GTPase, homolog 1; synapse defective 1, Rho GTPase, homolog 1 (C. elegans); synapse defective protein 1 homolog 1
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
GRCr8711,683,505 - 11,689,491 (+)NCBIGRCr8
mRatBN7.2711,032,931 - 11,038,917 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl711,032,898 - 11,039,869 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx713,851,843 - 13,857,840 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0715,729,230 - 15,735,227 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0713,607,127 - 13,613,134 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0714,037,646 - 14,043,632 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl714,037,620 - 14,043,779 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0714,191,914 - 14,201,067 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4712,586,155 - 12,592,141 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1712,586,131 - 12,592,156 (+)NCBI
Celera79,156,062 - 9,160,395 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:23791195   PMID:27917469  


Genomics

Comparative Map Data
Syde1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8711,683,505 - 11,689,491 (+)NCBIGRCr8
mRatBN7.2711,032,931 - 11,038,917 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl711,032,898 - 11,039,869 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx713,851,843 - 13,857,840 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0715,729,230 - 15,735,227 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0713,607,127 - 13,613,134 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0714,037,646 - 14,043,632 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl714,037,620 - 14,043,779 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0714,191,914 - 14,201,067 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4712,586,155 - 12,592,141 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1712,586,131 - 12,592,156 (+)NCBI
Celera79,156,062 - 9,160,395 (+)NCBICelera
Cytogenetic Map7q11NCBI
SYDE1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381915,107,401 - 15,114,974 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1915,107,401 - 15,114,985 (+)EnsemblGRCh38hg38GRCh38
GRCh371915,218,212 - 15,225,785 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361915,079,214 - 15,086,789 (+)NCBINCBI36Build 36hg18NCBI36
Celera1915,113,949 - 15,121,526 (+)NCBICelera
Cytogenetic Map19p13.12NCBI
HuRef1914,786,043 - 14,793,619 (+)NCBIHuRef
CHM1_11915,217,698 - 15,225,274 (+)NCBICHM1_1
T2T-CHM13v2.01915,232,344 - 15,239,918 (+)NCBIT2T-CHM13v2.0
Syde1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391078,420,336 - 78,427,798 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1078,420,337 - 78,427,798 (-)EnsemblGRCm39 Ensembl
GRCm381078,584,502 - 78,591,964 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1078,584,503 - 78,591,964 (-)EnsemblGRCm38mm10GRCm38
MGSCv371078,047,248 - 78,054,709 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361077,987,621 - 77,995,093 (-)NCBIMGSCv36mm8
Celera1079,606,719 - 79,614,175 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Syde1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554958,136,810 - 8,147,289 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554958,140,152 - 8,147,491 (-)NCBIChiLan1.0ChiLan1.0
SYDE1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22020,021,258 - 20,028,858 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11919,023,882 - 19,031,469 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01914,640,493 - 14,648,080 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11915,625,095 - 15,632,623 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1915,625,096 - 15,631,600 (+)Ensemblpanpan1.1panPan2
SYDE1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12047,021,789 - 47,028,606 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2047,021,775 - 47,028,714 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2046,872,562 - 46,879,385 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02047,514,235 - 47,521,060 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2047,514,240 - 47,521,055 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12046,746,333 - 46,753,156 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02047,165,399 - 47,172,222 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02047,436,664 - 47,443,487 (-)NCBIUU_Cfam_GSD_1.0
Syde1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118205,803,674 - 205,810,424 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365965,349,776 - 5,359,538 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365965,352,813 - 5,359,561 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYDE1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl262,447,037 - 62,453,949 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1262,447,030 - 62,453,944 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2262,008,057 - 62,014,927 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYDE1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1613,709,110 - 13,717,249 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl613,709,148 - 13,716,241 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660745,816,677 - 5,825,219 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Syde1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249012,191,241 - 2,197,877 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249012,191,219 - 2,197,786 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Syde1
33 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:152
Count of miRNA genes:109
Interacting mature miRNAs:120
Transcripts:ENSRNOT00000009606
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
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat

Markers in Region
RH129156  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2711,039,651 - 11,039,834 (+)MAPPERmRatBN7.2
Rnor_6.0714,044,367 - 14,044,549NCBIRnor6.0
Rnor_5.0714,200,850 - 14,201,032UniSTSRnor5.0
RGSC_v3.4712,592,876 - 12,593,058UniSTSRGSC3.4
Celera79,161,130 - 9,161,312UniSTS
RH 3.4 Map766.4UniSTS
Cytogenetic Map7q11UniSTS
RH138757  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2711,037,421 - 11,037,553 (+)MAPPERmRatBN7.2
Rnor_6.0714,042,137 - 14,042,268NCBIRnor6.0
Rnor_5.0714,198,620 - 14,198,751UniSTSRnor5.0
RGSC_v3.4712,590,646 - 12,590,777UniSTSRGSC3.4
Celera79,158,900 - 9,159,031UniSTS
Cytogenetic Map7q11UniSTS


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 37 14 4 7 4 6 23 33 11
Low 3 6 43 37 12 37 8 11 68 12 8 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000009606   ⟹   ENSRNOP00000009606
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl711,032,898 - 11,039,869 (+)Ensembl
Rnor_6.0 Ensembl714,037,620 - 14,043,779 (+)Ensembl
RefSeq Acc Id: NM_001191876   ⟹   NP_001178805
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8711,683,505 - 11,689,491 (+)NCBI
mRatBN7.2711,032,931 - 11,038,917 (+)NCBI
Rnor_6.0714,037,646 - 14,043,632 (+)NCBI
Rnor_5.0714,191,914 - 14,201,067 (+)NCBI
Celera79,156,062 - 9,160,395 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178805 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3ZZN9 (Get FASTA)   NCBI Sequence Viewer  
  EDL89449 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009606
  ENSRNOP00000009606.4
RefSeq Acc Id: NP_001178805   ⟸   NM_001191876
- UniProtKB: D3ZZN9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009606   ⟸   ENSRNOT00000009606
Protein Domains
C2   Rho-GAP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZZN9-F1-model_v2 AlphaFold D3ZZN9 1-735 view protein structure

Transcriptome

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

Promoters
RGD ID:13695064
Promoter ID:EPDNEW_R5589
Type:initiation region
Name:Syde1_1
Description:synapse defective Rho GTPase homolog 1
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_6.0714,037,618 - 14,037,678EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305857 AgrOrtholog
BioCyc Gene G2FUF-34838 BioCyc
Ensembl Genes ENSRNOG00000007307 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000009606 ENTREZGENE
  ENSRNOT00000009606.7 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.555.10 UniProtKB/Swiss-Prot
InterPro C2_dom UniProtKB/Swiss-Prot
  Rho_GTPase_activation_prot UniProtKB/Swiss-Prot
  RhoGAP_dom UniProtKB/Swiss-Prot
KEGG Report rno:362842 UniProtKB/Swiss-Prot
NCBI Gene 362842 ENTREZGENE
PANTHER RHO GTPASE-ACTIVATING PROTEIN 100F UniProtKB/Swiss-Prot
  RHO GTPASE-ACTIVATING PROTEIN SYDE1 UniProtKB/Swiss-Prot
Pfam RhoGAP UniProtKB/Swiss-Prot
PhenoGen Syde1 PhenoGen
PROSITE PS50004 UniProtKB/Swiss-Prot
  RHOGAP UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000007307 RatGTEx
SMART RhoGAP UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48350 UniProtKB/Swiss-Prot
UniProt D3ZZN9 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-05 Syde1  synapse defective Rho GTPase homolog 1  Syde1  synapse defective 1, Rho GTPase, homolog 1 (C. elegans)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Syde1  synapse defective 1, Rho GTPase, homolog 1 (C. elegans)   Syde1_predicted  synapse defective 1, Rho GTPase, homolog 1 (C. elegans) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Syde1_predicted  synapse defective 1, Rho GTPase, homolog 1 (C. elegans) (predicted)  RGD1305857_predicted  similar to hypothetical protein FLJ13511 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1305857_predicted  similar to hypothetical protein FLJ13511 (predicted)  LOC362842_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC362842_predicted  similar to hypothetical protein FLJ13511 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL