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

Gene ID: 66013, updated on 6-Jun-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

    UniProtKB/TrEMBL
    A6IQ19

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

    UniProtKB/TrEMBL
    A6IQ19

  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

    UniProtKB/TrEMBL
    A0A8I5ZZM9
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9QX73.1 GenPept UniProtKB/Swiss-Prot:Q9QX73

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