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 positive regulation of trophoblast cell migration 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; cytosol; and synaptic membrane. Orthologous to human SYDE1 (synapse defective Rho GTPase homolog 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; benzo[a]pyrene.
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 Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2711,032,931 - 11,038,917 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl711,032,898 - 11,039,869 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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


References

Additional References at PubMed
PMID:23791195   PMID:27917469  


Genomics

Comparative Map Data
Syde1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2711,032,931 - 11,038,917 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl711,032,898 - 11,039,869 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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.p13 Ensembl1915,107,401 - 15,114,985 (+)EnsemblGRCh38hg38GRCh38
GRCh371915,218,212 - 15,225,785 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361915,079,214 - 15,086,789 (+)NCBINCBI36hg18NCBI36
Celera1915,113,949 - 15,121,526 (+)NCBI
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 (+)NCBI
Syde1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391078,420,336 - 78,427,798 (-)NCBIGRCm39mm39
GRCm39 Ensembl1078,420,337 - 78,427,798 (-)Ensembl
GRCm381078,584,502 - 78,591,964 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1078,584,503 - 78,591,964 (-)EnsemblGRCm38mm10GRCm38
MGSCv371078,047,248 - 78,054,709 (-)NCBIGRCm37mm9NCBIm37
MGSCv361077,987,621 - 77,995,093 (-)NCBImm8
Celera1079,606,719 - 79,614,175 (-)NCBICelera
Cytogenetic Map10C1NCBI
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
PanPan1.11915,625,095 - 15,632,623 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1915,625,096 - 15,631,600 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01914,640,493 - 14,648,080 (+)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.02047,514,235 - 47,521,060 (-)NCBI
ROS_Cfam_1.0 Ensembl2047,514,240 - 47,521,055 (-)Ensembl
UMICH_Zoey_3.12046,746,333 - 46,753,156 (-)NCBI
UNSW_CanFamBas_1.02047,165,399 - 47,172,222 (-)NCBI
UU_Cfam_GSD_1.02047,436,664 - 47,443,487 (-)NCBI
Syde1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118205,803,674 - 205,810,424 (-)NCBI
SpeTri2.0NW_0049365965,352,813 - 5,359,561 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYDE1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl262,447,036 - 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 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl613,709,148 - 13,716,241 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660745,816,677 - 5,825,219 (-)NCBIVero_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_1.0hetGla2
HetGla 1.0NW_0046249012,191,219 - 2,197,786 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
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


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

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.


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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009606   ⟹   ENSRNOP00000009606
RefSeq Status:
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
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  
Reference Sequences
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

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 14195785 14195786 C T snv SDLEF7/Barth (UDEL)


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 Protein ENSRNOP00000009606 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000009606 ENTREZGENE, 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
Pfam RhoGAP UniProtKB/Swiss-Prot
PhenoGen Syde1 PhenoGen
PROSITE PS50004 UniProtKB/Swiss-Prot
  RHOGAP UniProtKB/Swiss-Prot
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