Syngap1 (synaptic Ras GTPase activating protein 1) - Rat Genome Database

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Gene: Syngap1 (synaptic Ras GTPase activating protein 1) Rattus norvegicus
Analyze
Symbol: Syngap1
Name: synaptic Ras GTPase activating protein 1
RGD ID: 621090
Description: Exhibits GTPase activator activity and protein kinase binding activity. Involved in negative regulation of Ras protein signal transduction and regulation of synaptic plasticity. Localizes to glutamatergic synapse and postsynaptic density, intracellular component. Human ortholog(s) of this gene implicated in autosomal dominant non-syndromic intellectual disability 5. Orthologous to human SYNGAP1 (synaptic Ras GTPase activating protein 1); PARTICIPATES IN calcium/calmodulin dependent kinase 2 signaling pathway; INTERACTS WITH 4-[1-hydroxy-2-[4-(phenylmethyl)-1-piperidinyl]propyl]phenol; acetamide; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: neuronal RasGAP; p135 SynGAP; ras GTPase-activating protein SynGAP; ras/Rap GTPase-activating protein SynGAP; synaptic Ras GTPase activating protein 1 homolog; synaptic Ras GTPase activating protein 1 homolog (rat); synaptic Ras GTPase-activating protein 1; synaptic Ras-GAP 1; Syngap
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2205,026,366 - 5,056,659 (+)NCBI
Rnor_6.0 Ensembl205,535,432 - 5,564,437 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0205,535,434 - 5,564,657 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0207,594,614 - 7,623,865 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,178,523 - 5,208,449 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1205,191,049 - 5,207,973 (+)NCBI
Celera206,608,780 - 6,637,810 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11489946   PMID:12063253   PMID:12427827   PMID:12598599   PMID:15014045   PMID:15312654   PMID:15470153   PMID:15500970   PMID:15733080   PMID:15781580   PMID:16452659   PMID:17114649  
PMID:17646177   PMID:18417361   PMID:18824155   PMID:20131911   PMID:22871113   PMID:25533468   PMID:25931508   PMID:26124704   PMID:27565345   PMID:29476059   PMID:30053369  


Genomics

Comparative Map Data
Syngap1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2205,026,366 - 5,056,659 (+)NCBI
Rnor_6.0 Ensembl205,535,432 - 5,564,437 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0205,535,434 - 5,564,657 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0207,594,614 - 7,623,865 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,178,523 - 5,208,449 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1205,191,049 - 5,207,973 (+)NCBI
Celera206,608,780 - 6,637,810 (+)NCBICelera
Cytogenetic Map20p12NCBI
SYNGAP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl633,419,661 - 33,453,689 (+)EnsemblGRCh38hg38GRCh38
GRCh38633,420,065 - 33,453,689 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37633,387,842 - 33,421,466 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36633,495,825 - 33,529,444 (+)NCBINCBI36hg18NCBI36
Celera634,942,270 - 34,975,892 (+)NCBI
Cytogenetic Map6p21.32NCBI
HuRef633,129,996 - 33,162,361 (+)NCBIHuRef
CHM1_1633,389,741 - 33,423,358 (+)NCBICHM1_1
Syngap1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391727,160,186 - 27,191,408 (+)NCBIGRCm39mm39
GRCm39 Ensembl1727,160,227 - 27,191,408 (+)Ensembl
GRCm381726,941,212 - 26,972,434 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1726,941,253 - 26,972,434 (+)EnsemblGRCm38mm10GRCm38
MGSCv371727,078,397 - 27,107,590 (+)NCBIGRCm37mm9NCBIm37
MGSCv361726,669,086 - 26,698,234 (+)NCBImm8
Celera1727,478,075 - 27,507,298 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
Syngap1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554371,950,602 - 1,979,251 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554371,950,559 - 1,981,004 (+)NCBIChiLan1.0ChiLan1.0
SYNGAP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1634,111,285 - 34,144,490 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl634,110,652 - 34,144,490 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0632,999,408 - 33,033,067 (+)NCBIMhudiblu_PPA_v0panPan3
SYNGAP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1122,829,274 - 2,862,888 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl122,829,306 - 2,851,432 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha122,910,079 - 2,943,658 (+)NCBI
ROS_Cfam_1.0123,162,881 - 3,194,514 (+)NCBI
UMICH_Zoey_3.1122,828,036 - 2,861,597 (+)NCBI
UNSW_CanFamBas_1.0122,909,144 - 2,942,686 (+)NCBI
UU_Cfam_GSD_1.0123,007,257 - 3,040,837 (+)NCBI
Syngap1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494638,485,483 - 38,513,743 (+)NCBI
SpeTri2.0NW_00493647625,446,524 - 25,474,793 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYNGAP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl729,723,774 - 29,753,934 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1729,723,745 - 29,752,351 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2734,341,195 - 34,373,397 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYNGAP1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11738,612,777 - 38,646,382 (-)NCBI
ChlSab1.1 Ensembl1738,617,679 - 38,646,192 (-)Ensembl
Vero_WHO_p1.0NW_02366604433,268,732 - 33,302,381 (+)NCBI
Syngap1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475423,367,585 - 23,396,643 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2020187706567419Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2031518156896013Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2031518156896013Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2040391135875448Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2048554689899946Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RChigh CD8 T cell count to CD45RClow CD8 T cell count ratio (CMO:0001990)20485546810800530Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:315
Count of miRNA genes:117
Interacting mature miRNAs:145
Transcripts:ENSRNOT00000000572, ENSRNOT00000040859, ENSRNOT00000042332
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 26 4 4 4 74 20 30
Low 3 16 41 29 15 29 4 7 15 11 11 4
Below cutoff 1 12 8 4 8 4 4 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000572   ⟹   ENSRNOP00000000572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,535,547 - 5,564,437 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000040859   ⟹   ENSRNOP00000044041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,535,432 - 5,563,920 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,546,152 - 5,564,250 (+)Ensembl
RefSeq Acc Id: NM_001113409   ⟹   NP_001106880
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,037,078 - 5,056,659 (+)NCBI
Rnor_6.0205,546,152 - 5,564,657 (+)NCBI
Rnor_5.0207,594,614 - 7,623,865 (+)NCBI
RGSC_v3.4205,178,523 - 5,208,449 (+)RGD
Celera206,619,335 - 6,637,810 (+)NCBI
Sequence:
RefSeq Acc Id: NM_181092   ⟹   NP_851606
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,026,366 - 5,056,659 (+)NCBI
Rnor_6.0205,535,434 - 5,564,657 (+)NCBI
Rnor_5.0207,594,614 - 7,623,865 (+)NCBI
RGSC_v3.4205,178,523 - 5,208,449 (+)RGD
Celera206,608,780 - 6,637,810 (+)RGD
Sequence:
RefSeq Acc Id: NR_144519
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,026,366 - 5,056,659 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_851606   ⟸   NM_181092
- Peptide Label: isoform 1
- UniProtKB: F1LQW8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001106880   ⟸   NM_001113409
- Peptide Label: isoform 2
- Sequence:
RefSeq Acc Id: ENSRNOP00000000572   ⟸   ENSRNOT00000000572
RefSeq Acc Id: ENSRNOP00000044041   ⟸   ENSRNOT00000040859
Protein Domains
C2   PH   Ras-GAP

Transcriptome

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

Promoters
RGD ID:13701424
Promoter ID:EPDNEW_R11946
Type:initiation region
Name:Syngap1_1
Description:synaptic Ras GTPase activating protein 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_6.0205,535,351 - 5,535,411EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 7605851 7605852 C T snv SBH/Ygl (MCW), LH/MavRrrc (KNAW), LN/MavRrrc (KNAW), SBH/Ygl (KNAW), LE/Stm (KyushuU), BUF/N (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), M520/N (KNAW), WKY/N (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 5546643 5546644 C T snv SBH/Ygl (MCW), Buf/N (MCW), M520/N (MCW), SBH/Ygl (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LE/Stm (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621090 AgrOrtholog
Ensembl Genes ENSRNOG00000000483 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000572 UniProtKB/TrEMBL
  ENSRNOP00000044041 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000572 UniProtKB/TrEMBL
  ENSRNOT00000040859 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000092424 ENTREZGENE
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro C2_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DUF3498 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ras_GTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RasGAP_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RasGAP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rho_GTPase_activation_prot UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SynGAP_PH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 192117 ENTREZGENE
PANTHER PTHR10194 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF3498 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00168 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RasGAP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Syngap1 PhenoGen
PROSITE PH_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PS50004 UniProtKB/Swiss-Prot
  RAS_GTPASE_ACTIV_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RAS_GTPASE_ACTIV_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART RasGAP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00233 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48350 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt D3ZCL8_RAT UniProtKB/TrEMBL
  F1LQW8 ENTREZGENE, UniProtKB/TrEMBL
  Q9QUH6 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O88449 UniProtKB/Swiss-Prot
  Q9ESK6 UniProtKB/Swiss-Prot
  Q9ET81 UniProtKB/Swiss-Prot
  Q9QX02 UniProtKB/Swiss-Prot
  Q9QX06 UniProtKB/Swiss-Prot
  Q9QX12 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-01 Syngap1  synaptic Ras GTPase activating protein 1  Syngap1  synaptic Ras GTPase activating protein 1 homolog (rat)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Syngap1  synaptic Ras GTPase activating protein 1 homolog (rat)    synaptic Ras GTPase activating protein 1  Name updated 1299863 APPROVED
2002-08-07 Syngap1  synaptic Ras GTPase activating protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization binds PSD-95 and colocalizes with NMDA receptors to hippocampla neuron synapses 634128
gene_mapping maps to the MHC RT1 complex 1300431