Arhgef9 (Cdc42 guanine nucleotide exchange factor 9) - Rat Genome Database
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Gene: Arhgef9 (Cdc42 guanine nucleotide exchange factor 9) Rattus norvegicus
Analyze
Symbol: Arhgef9
Name: Cdc42 guanine nucleotide exchange factor 9
RGD ID: 620719
Description: Predicted to have guanyl-nucleotide exchange factor activity. Involved in receptor clustering. Localizes to several cellular components, including GABA-ergic synapse; glycinergic synapse; and postsynaptic specialization. Human ortholog(s) of this gene implicated in early infantile epileptic encephalopathy 8. Orthologous to human ARHGEF9 (Cdc42 guanine nucleotide exchange factor 9); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 3,4-methylenedioxymethamphetamine; benzo[a]pyrene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cdc42 guanine nucleotide exchange factor (GEF) 9; collybistin I; rac/Cdc42 guanine nucleotide exchange factor 9; rho guanine nucleotide exchange factor 9
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
mRatBN7.2X59,919,560 - 60,077,538 (-)NCBI
Rnor_6.0 EnsemblX64,248,278 - 64,428,592 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X64,249,576 - 64,428,444 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X65,150,714 - 65,329,116 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X82,594,347 - 82,754,179 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X82,667,647 - 82,827,471 (-)NCBI
CeleraX60,352,255 - 60,508,707 (-)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:11727829   PMID:15215304   PMID:16616186   PMID:17690689   PMID:21540179   PMID:22659578   PMID:22778260   PMID:24297911   PMID:27609886  


Genomics

Comparative Map Data
Arhgef9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X59,919,560 - 60,077,538 (-)NCBI
Rnor_6.0 EnsemblX64,248,278 - 64,428,592 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X64,249,576 - 64,428,444 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X65,150,714 - 65,329,116 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X82,594,347 - 82,754,179 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X82,667,647 - 82,827,471 (-)NCBI
CeleraX60,352,255 - 60,508,707 (-)NCBICelera
Cytogenetic MapXq22NCBI
ARHGEF9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX63,634,967 - 63,809,274 (-)EnsemblGRCh38hg38GRCh38
GRCh38X63,634,967 - 63,785,546 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X62,854,847 - 63,005,094 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh37X62,854,847 - 63,005,426 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X62,771,573 - 62,891,718 (-)NCBINCBI36hg18NCBI36
Build 34X62,637,868 - 62,758,014NCBI
CeleraX63,201,689 - 63,352,277 (-)NCBI
Cytogenetic MapXq11.1NCBI
HuRefX56,681,875 - 56,830,928 (-)NCBIHuRef
CHM1_1X62,747,364 - 62,897,940 (-)NCBICHM1_1
Arhgef9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X94,092,536 - 94,240,801 (-)NCBIGRCm39mm39
GRCm38X95,048,930 - 95,196,853 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX95,048,935 - 95,196,856 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X92,244,283 - 92,361,825 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X91,251,663 - 91,369,205 (-)NCBImm8
CeleraX82,072,839 - 82,190,049 (-)NCBICelera
Cytogenetic MapXC3NCBI
Arhgef9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554754,017,632 - 4,214,563 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554754,020,922 - 4,214,464 (-)NCBIChiLan1.0ChiLan1.0
ARHGEF9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X62,862,115 - 63,010,088 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX62,862,115 - 63,010,512 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X52,779,238 - 52,946,480 (-)NCBIMhudiblu_PPA_v0panPan3
ARHGEF9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX49,101,985 - 49,313,136 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X49,101,034 - 49,312,797 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Arhgef9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366353,817,034 - 3,956,928 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ARHGEF9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X50,159,912 - 50,578,020 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X56,579,846 - 56,756,238 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ARHGEF9
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X54,029,085 - 54,214,760 (-)NCBI
ChlSab1.1 EnsemblX54,029,084 - 54,153,172 (-)Ensembl
Arhgef9
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248983,058,094 - 3,301,738 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
70221Bp56Blood pressure QTL 564.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X6139809770352120Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:186
Count of miRNA genes:141
Interacting mature miRNAs:161
Transcripts:ENSRNOT00000042654, ENSRNOT00000063861
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.


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 72 16 20
Low 3 43 56 40 19 40 8 11 2 19 15 11 8
Below cutoff 1 1 1 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000042654
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX64,273,599 - 64,367,255 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000063861
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX64,272,705 - 64,428,444 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076190
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX64,248,278 - 64,250,792 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076965
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX64,272,705 - 64,428,444 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084678
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX64,250,870 - 64,428,592 (-)Ensembl
RefSeq Acc Id: NM_023957   ⟹   NP_076447
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X59,920,858 - 60,077,513 (-)NCBI
Rnor_6.0X64,249,576 - 64,428,444 (-)NCBI
Rnor_5.0X65,150,714 - 65,329,116 (-)NCBI
RGSC_v3.4X82,594,347 - 82,754,179 (-)RGD
CeleraX60,352,255 - 60,508,707 (-)RGD
Sequence:
RefSeq Acc Id: XM_039100035   ⟹   XP_038955963
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X59,919,560 - 60,077,538 (-)NCBI
RefSeq Acc Id: XM_039100036   ⟹   XP_038955964
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X59,919,560 - 60,049,817 (-)NCBI
RefSeq Acc Id: XM_039100037   ⟹   XP_038955965
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X59,919,560 - 60,049,817 (-)NCBI
RefSeq Acc Id: XM_039100038   ⟹   XP_038955966
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X59,919,560 - 60,049,817 (-)NCBI
RefSeq Acc Id: XM_039100039   ⟹   XP_038955967
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X59,919,560 - 60,047,500 (-)NCBI
RefSeq Acc Id: XM_039100040   ⟹   XP_038955968
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X59,919,560 - 60,077,538 (-)NCBI
RefSeq Acc Id: XM_039100041   ⟹   XP_038955969
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X59,919,560 - 60,077,538 (-)NCBI
RefSeq Acc Id: XM_039100042   ⟹   XP_038955970
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X59,919,560 - 60,077,538 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_076447   ⟸   NM_023957
- UniProtKB: Q9QX73 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_038955969   ⟸   XM_039100041
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038955970   ⟸   XM_039100042
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038955963   ⟸   XM_039100035
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955968   ⟸   XM_039100040
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038955966   ⟸   XM_039100038
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038955965   ⟸   XM_039100037
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955964   ⟸   XM_039100036
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955967   ⟸   XM_039100039
- Peptide Label: isoform X4
Protein Domains
DH   PH   SH3

Transcriptome

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


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)
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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620719 AgrOrtholog
Ensembl Genes ENSRNOG00000007733 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000063861 ENTREZGENE
Gene3D-CATH 1.20.900.10 UniProtKB/Swiss-Prot
  2.30.29.30 UniProtKB/Swiss-Prot
InterPro ARHGEF9_SH3 UniProtKB/Swiss-Prot
  DBL_dom_sf UniProtKB/Swiss-Prot
  DH-domain UniProtKB/Swiss-Prot
  PH-like_dom_sf UniProtKB/Swiss-Prot
  PH_domain UniProtKB/Swiss-Prot
  SH3-like_dom_sf UniProtKB/Swiss-Prot
  SH3_domain UniProtKB/Swiss-Prot
KEGG Report rno:66013 UniProtKB/Swiss-Prot
NCBI Gene 66013 ENTREZGENE
Pfam PF00169 UniProtKB/Swiss-Prot
  RhoGEF UniProtKB/Swiss-Prot
  SH3_1 UniProtKB/Swiss-Prot
PhenoGen Arhgef9 PhenoGen
PROSITE DH_2 UniProtKB/Swiss-Prot
  PH_DOMAIN UniProtKB/Swiss-Prot
  SH3 UniProtKB/Swiss-Prot
SMART RhoGEF UniProtKB/Swiss-Prot
  SH3 UniProtKB/Swiss-Prot
  SM00233 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48065 UniProtKB/Swiss-Prot
  SSF50044 UniProtKB/Swiss-Prot
UniProt ARHG9_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9ER22 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-19 Arhgef9  Cdc42 guanine nucleotide exchange factor 9  Arhgef9  Cdc42 guanine nucleotide exchange factor (GEF) 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Arhgef9  Cdc42 guanine nucleotide exchange factor (GEF) 9    collybistin I  Name updated 1299863 APPROVED
2002-08-07 Arhgef9  collybistin I      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_product belongs to the family of dbl-like GDP/GTP exchange factors (GEFs) 632270