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    Arhgef9 Cdc42 guanine nucleotide exchange factor 9 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 66013, updated on 13-Apr-2024

    Summary

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    Symbol
    Arhgef9provided by RGD
    Full Name
    Cdc42 guanine nucleotide exchange factor 9provided by RGD
    Primary source
    RGD:620719
    See related
    Ensembl:ENSRNOG00000007733 AllianceGenome:RGD:620719
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity. Involved in receptor clustering. Located in cell cortex. Is active in GABA-ergic synapse; glycinergic synapse; and postsynaptic specialization. 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 Brain (RPKM 454.6), Heart (RPKM 52.2) and 4 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Arhgef9 in Genome Data Viewer
    Location:
    Xq22
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (63929168..64087267, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (59919560..60077538, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (64249576..64428444, complement)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene 40S ribosomal protein S10 pseudogene Neighboring gene spindlin family, member 4 Neighboring gene uncharacterized LOC134484135 Neighboring gene U4 spliceosomal RNA Neighboring gene sperm motility kinase X like, pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Collybistin SH3-protein isoforms are expressed in the rat brain promoting gephyrin and GABA-A receptor clustering at GABAergic synapses. George S, et al. J Neurochem, 2021 May. PMID 33316079
    2. Effects of distinct collybistin isoforms on the formation of GABAergic synapses in hippocampal neurons. Körber C, et al. Mol Cell Neurosci, 2012 Jul. PMID 22659578
    3. Differential regulation of the postsynaptic clustering of γ-aminobutyric acid type A (GABAA) receptors by collybistin isoforms. Chiou TT, et al. J Biol Chem, 2011 Jun 24. PMID 21540179, Free PMC Article
    4. 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
    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 (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Collybistin SH3-protein isoforms are expressed in the rat brain promoting gephyrin and GABA-A receptor clustering at GABAergic synapses.
      Title: Collybistin SH3-protein isoforms are expressed in the rat brain promoting gephyrin and GABA-A receptor clustering at GABAergic synapses.
    2. The enhancement of Cb-induced gephyrin clustering by GTP-TC10 does not depend on the guanine nucleotide exchange activity of Cb but involves an interaction that resembles reported interactions of other small GTPases with their effectors
      Title: Collybistin activation by GTP-TC10 enhances postsynaptic gephyrin clustering and hippocampal GABAergic neurotransmission.
    3. Collybistin (Cb) knock-down induced impairment in GABAergic neurotransmission could be rescued by the expression of any of the Cb isoforms, independent of their C-termini or the presence of the SH3-domain in the N-terminal region.
      Title: Effects of distinct collybistin isoforms on the formation of GABAergic synapses in hippocampal neurons.
    4. Phosphorylation of gephyrin in hippocampal neurons by cyclin-dependent kinase CDK5 at Ser-270 is dependent on collybistin.
      Title: Phosphorylation of gephyrin in hippocampal neurons by cyclin-dependent kinase CDK5 at Ser-270 is dependent on collybistin.
    5. 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.
    6. in transfected hippocampal neurons, all collybistin isoforms (CB2(SH3+), CB2(SH3-), CB3(SH3+), and CB3(SH3-)) target to and concentrate at GABAergic postsynapses
      Title: Differential regulation of the postsynaptic clustering of γ-aminobutyric acid type A (GABAA) receptors by collybistin isoforms.
    7. translocates gephyrin to submembrane microaggregates
      Title: The GDP-GTP exchange factor collybistin: an essential determinant of neuronal gephyrin clustering.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in receptor clustering IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of postsynaptic specialization assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of postsynaptic specialization assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell cortex IDA
    Inferred from Direct Assay
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynaptic density ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in postsynaptic density ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in postsynaptic specialization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in postsynaptic specialization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    rho guanine nucleotide exchange factor 9
    Names
    Cdc42 guanine nucleotide exchange factor (GEF) 9
    collybistin I
    rac/Cdc42 guanine nucleotide exchange factor 9
    rho guanine nucleotide exchange factor 9-like

    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_001393743.1 → NP_001380672.1  rho guanine nucleotide exchange factor 9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A6IQ19
      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

    2. NM_023957.2 → NP_076447.2  rho guanine nucleotide exchange factor 9 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/Swiss-Prot
      Q9ER22, Q9QX73
      UniProtKB/TrEMBL
      A0A8I5ZLM2, A6IQ20
      Related
      ENSRNOP00000078766.1, ENSRNOT00000063861.4
      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

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086039.1 Reference GRCr8

      Range
      63929168..64087267 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039100035.2 → XP_038955963.1  rho guanine nucleotide exchange factor 9 isoform X1

      UniProtKB/TrEMBL
      A6IQ19
      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_039100041.1 → XP_038955969.1  rho guanine nucleotide exchange factor 9 isoform X6

      UniProtKB/TrEMBL
      A6IQ21
      Conserved Domains (2) summary
      smart00325
      Location:54 → 233
      RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases
      cd01224
      Location:238 → 377
      PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain

    3. XM_039100037.2 → XP_038955965.1  rho guanine nucleotide exchange factor 9 isoform X3

      UniProtKB/TrEMBL
      A6IQ19
      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

    4. XM_039100036.2 → XP_038955964.1  rho guanine nucleotide exchange factor 9 isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZMR8, A6IQ19
      Related
      ENSRNOP00000079409.1
      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

    5. XM_063280289.1 → XP_063136359.1  rho guanine nucleotide exchange factor 9 isoform X4

    6. XM_063280288.1 → XP_063136358.1  rho guanine nucleotide exchange factor 9 isoform X4

    7. XM_039100039.2 → XP_038955967.1  rho guanine nucleotide exchange factor 9 isoform X4

      UniProtKB/TrEMBL
      A6IQ19
      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

    8. XM_039100040.2 → XP_038955968.1  rho guanine nucleotide exchange factor 9 isoform X5

      UniProtKB/TrEMBL
      A6IQ22
      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

    9. XM_063280290.1 → XP_063136360.1  rho guanine nucleotide exchange factor 9 isoform X7

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9QX73.1 GenPept UniProtKB/Swiss-Prot:Q9QX73

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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