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Arhgef9 CDC42 guanine nucleotide exchange factor 9 [ Mus musculus (house mouse) ]

Gene ID: 236915, updated on 2-Nov-2024

Summary

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Official Symbol
Arhgef9provided by MGI
Official Full Name
CDC42 guanine nucleotide exchange factor 9provided by MGI
Primary source
MGI:MGI:2442233
See related
Ensembl:ENSMUSG00000025656 AllianceGenome:MGI:2442233
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
9630036L12Rik
Summary
Predicted to enable guanyl-nucleotide exchange factor activity. Involved in regulation of postsynaptic specialization assembly. Located in postsynaptic density. Is active in GABA-ergic synapse. Is expressed in several structures, including central nervous system; dorsal root ganglion; and ear. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 8. Orthologous to human ARHGEF9 (Cdc42 guanine nucleotide exchange factor 9). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in frontal lobe adult (RPKM 27.9), cortex adult (RPKM 25.1) and 8 other tissues See more
Orthologs
human all
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Genomic context

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See Arhgef9 in Genome Data Viewer
Location:
X C3; X 41.85 cM
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (94092536..94240801, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (95048930..95196853, complement)

Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_47564 Neighboring gene germ cell-less homolog 1 pseudogene Neighboring gene spindlin family, member 4 Neighboring gene STARR-seq mESC enhancer starr_47565 Neighboring gene STARR-seq mESC enhancer starr_47566 Neighboring gene adenylate kinase 1 pseudogene Neighboring gene NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 4 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. The α3 subunit of GABA(A) receptors promotes formation of inhibitory synapses in the absence of collybistin. Wagner S, et al. J Biol Chem, 2021 Jan-Jun. PMID 33901490, Free PMC Article
  2. Increased network excitability and impaired induction of long-term potentiation in the dentate gyrus of collybistin-deficient mice in vivo. Jedlicka P, et al. Mol Cell Neurosci, 2009 May. PMID 19236916
  3. Developmental seizures and mortality result from reducing GABA(A) receptor α2-subunit interaction with collybistin. Hines RM, et al. Nat Commun, 2018 Aug 7. PMID 30087324, Free PMC Article
  4. RhoGEF9 splice isoforms influence neuronal maturation and synapse formation downstream of α2 GABAA receptors. de Groot C, et al. PLoS Genet, 2017 Oct. PMID 29069083, Free PMC Article
  5. Impaired GABAergic transmission and altered hippocampal synaptic plasticity in collybistin-deficient mice. Papadopoulos T, et al. EMBO J, 2007 Sep 5. PMID 17690689, Free PMC Article

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Collybistin binds the GABAAR-alpha2-subunit with high affinity
    Title: Developmental seizures and mortality result from reducing GABA(A) receptor α2-subunit interaction with collybistin.
  2. Results uncover previously unexpected role for CB isoforms downstream of alpha2-containing GABAARs during neuron maturation in a Cdc42 dependent mechanism.
    Title: RhoGEF9 splice isoforms influence neuronal maturation and synapse formation downstream of α2 GABAA receptors.
  3. Within this network, collybistin can adopt open/active and closed/inactive conformations to act as a switchable adaptor that links gephyrin to plasma membrane phosphoinositides.
    Title: A conformational switch in collybistin determines the differentiation of inhibitory postsynapses.
  4. data show that collybistin co-clusters with gephyrin and GABA(A) Rs in synaptic puncta and is recruited to postsynaptic specializations early during synapse development; it co-localizes with GABA(A) Rs containing the alpha1, alpha2, or alpha3 subunits
    Title: Selective localization of collybistin at a subset of inhibitory synapses in brain circuits.
  5. The results of this study provided evidence that the formation of gephyrin scaffolds at inhibitory synapses requires an intact Cb II PH-domain but is Cdc42-independent.
    Title: PH-domain-driven targeting of collybistin but not Cdc42 activation is required for synaptic gephyrin clustering.
  6. Data provide the first evidence that collybistin deficiency leads to significant changes of GABAergic inhibition, network excitability and synaptic plasticity in vivo.
    Title: Increased network excitability and impaired induction of long-term potentiation in the dentate gyrus of collybistin-deficient mice in vivo.
  7. The resolution crystal structure of the Cdc42-collybistin II complex reveals a novel conformation of the switch I region of Cdc42, and biochemical data indicate that gephyrin negatively regulates collybistin activity.
    Title: The crystal structure of Cdc42 in complex with collybistin II, a gephyrin-interacting guanine nucleotide exchange factor.
  8. Cb is essential for gephyrin-dependent clustering of a specific set of GABA(A) receptors, but not required for glycine receptor postsynaptic localization.
    Title: Impaired GABAergic transmission and altered hippocampal synaptic plasticity in collybistin-deficient mice.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 
  • Targeted (2)  1 citation

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in receptor clustering ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of postsynaptic specialization assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of postsynaptic specialization assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of postsynaptic specialization assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within small GTPase-mediated signal transduction TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in GABA-ergic synapse IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in GABA-ergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in GABA-ergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
is_active_in GABA-ergic synapse ISO
Inferred from Sequence Orthology
more info
  
located_in cell cortex ISO
Inferred from Sequence Orthology
more info
  
located_in cell cortex TAS
Traceable Author Statement
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
is_active_in glycinergic synapse ISO
Inferred from Sequence Orthology
more info
  
located_in postsynaptic density IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in postsynaptic specialization IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in postsynaptic specialization ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
rho guanine nucleotide exchange factor 9
Names
CDC42 guanine nucleotide exchange factor (GEF) 9
collybistin
rac/Cdc42 guanine nucleotide exchange factor 9

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001033329.4 → NP_001028501.1  rho guanine nucleotide exchange factor 9 isoform a

    See identical proteins and their annotated locations for NP_001028501.1

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092
    Consensus CDS
    CCDS53137.1
    UniProtKB/Swiss-Prot
    B1AXI3, B1AXI5, B9EJ88, Q3TQ60, Q3UTH8, Q80U06, Q8CAF9
    UniProtKB/TrEMBL
    B1AXI4
    Related
    ENSMUSP00000109510.2, ENSMUST00000113878.8
    Conserved Domains (3) summary
    cd11975
    Location:7 → 68
    SH3_ARHGEF9; Src homology 3 domain of the Rho guanine nucleotide exchange factor ARHGEF9
    smart00325
    Location:107 → 286
    RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases
    cd01224
    Location:291 → 430
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain

  2. NM_001290384.2 → NP_001277313.1  rho guanine nucleotide exchange factor 9 isoform b

    See identical proteins and their annotated locations for NP_001277313.1

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092
    Consensus CDS
    CCDS72409.1
    UniProtKB/TrEMBL
    B1AXI4
    Related
    ENSMUSP00000138668.2, ENSMUST00000182001.8
    Conserved Domains (3) summary
    smart00325
    Location:86 → 265
    RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases
    cd01224
    Location:270 → 409
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    cl17036
    Location:1 → 47
    SH3; Src Homology 3 domain superfamily

  3. NM_001290385.2 → NP_001277314.1  rho guanine nucleotide exchange factor 9 isoform b

    See identical proteins and their annotated locations for NP_001277314.1

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092
    Consensus CDS
    CCDS72409.1
    UniProtKB/TrEMBL
    B1AXI4
    Related
    ENSMUSP00000109508.2, ENSMUST00000113876.9
    Conserved Domains (3) summary
    smart00325
    Location:86 → 265
    RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases
    cd01224
    Location:270 → 409
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    cl17036
    Location:1 → 47
    SH3; Src Homology 3 domain superfamily

  4. NM_001405901.1 → NP_001392830.1  rho guanine nucleotide exchange factor 9 isoform c

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  5. NM_001405902.1 → NP_001392831.1  rho guanine nucleotide exchange factor 9 isoform d

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092
    Related
    ENSMUSP00000109516.2, ENSMUST00000113884.8

  6. NM_001405903.1 → NP_001392832.1  rho guanine nucleotide exchange factor 9 isoform e

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  7. NM_001405904.1 → NP_001392833.1  rho guanine nucleotide exchange factor 9 isoform f

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  8. NM_001405905.1 → NP_001392834.1  rho guanine nucleotide exchange factor 9 isoform a

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092
    UniProtKB/Swiss-Prot
    B1AXI3, B1AXI5, B9EJ88, Q3TQ60, Q3UTH8, Q80U06, Q8CAF9

  9. NM_001405906.1 → NP_001392835.1  rho guanine nucleotide exchange factor 9 isoform g

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092
    Related
    ENSMUSP00000109515.2, ENSMUST00000113883.8

  10. NM_001405907.1 → NP_001392836.1  rho guanine nucleotide exchange factor 9 isoform h

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  11. NM_001405908.1 → NP_001392837.1  rho guanine nucleotide exchange factor 9 isoform b

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  12. NM_001405909.1 → NP_001392838.1  rho guanine nucleotide exchange factor 9 isoform b

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  13. NM_001405910.1 → NP_001392839.1  rho guanine nucleotide exchange factor 9 isoform i

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  14. NM_001405911.1 → NP_001392840.1  rho guanine nucleotide exchange factor 9 isoform j

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  15. NM_001405912.1 → NP_001392841.1  rho guanine nucleotide exchange factor 9 isoform k

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  16. NM_001405913.1 → NP_001392842.1  rho guanine nucleotide exchange factor 9 isoform l

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  17. NM_001405914.1 → NP_001392843.1  rho guanine nucleotide exchange factor 9 isoform o

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  18. NM_001405915.1 → NP_001392844.1  rho guanine nucleotide exchange factor 9 isoform m

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092
    Related
    ENSMUSP00000109505.2, ENSMUST00000113873.9

  19. NM_001405916.1 → NP_001392845.1  rho guanine nucleotide exchange factor 9 isoform n

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  20. NM_001405917.1 → NP_001392846.1  rho guanine nucleotide exchange factor 9 isoform n

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

  21. NM_001405918.1 → NP_001392847.1  rho guanine nucleotide exchange factor 9 isoform n

    Status: VALIDATED

    Source sequence(s)
    AL807821, BX470092

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000086.8 Reference GRCm39 C57BL/6J

    Range
    94092536..94240801 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030251325.2 → XP_030107185.1  rho guanine nucleotide exchange factor 9 isoform X9

    UniProtKB/TrEMBL
    A0A0G2JE35
    Related
    ENSMUSP00000138258.2, ENSMUST00000128565.8
    Conserved Domains (3) summary
    cd11975
    Location:14 → 75
    SH3_ARHGEF9; Src homology 3 domain of the Rho guanine nucleotide exchange factor ARHGEF9
    smart00325
    Location:114 → 293
    RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases
    cd01224
    Location:298 → 437
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain

  2. XM_036161929.1 → XP_036017822.1  rho guanine nucleotide exchange factor 9 isoform X6

    UniProtKB/TrEMBL
    A0A0G2JE35
    Conserved Domains (3) summary
    cd11975
    Location:1 → 47
    SH3_ARHGEF9; Src homology 3 domain of the Rho guanine nucleotide exchange factor ARHGEF9
    smart00325
    Location:86 → 265
    RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases
    cd01224
    Location:270 → 409
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain

  3. XM_011247585.3 → XP_011245887.1  rho guanine nucleotide exchange factor 9 isoform X8

    UniProtKB/TrEMBL
    S4R1K5
    Conserved Domains (3) summary
    smart00325
    Location:86 → 265
    RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases
    cd01224
    Location:270 → 409
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    cl17036
    Location:1 → 47
    SH3; Src Homology 3 domain superfamily
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q3UTH8.1 GenPept UniProtKB/Swiss-Prot:Q3UTH8

Gene LinkOut

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