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

    Gene ID: 236915, updated on 12-May-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 GABA-ergic synapse and postsynaptic density. 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, Apr 2022]
    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
    • 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. Selective localization of collybistin at a subset of inhibitory synapses in brain circuits. Patrizi A, et al. J Comp Neurol, 2012 Jan 1. PMID 21681748

    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 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		  
    located_in synapse IEA
    Inferred from Electronic Annotation
    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 l

      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

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