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

Summary

Symbol: Arhgef9provided by RGD
Full Name: Cdc42 guanine nucleotide exchange factor 9provided by RGD
Primary source: RGD:620719
See related: EnsemblRapid: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, Nov 2024]
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

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_086039.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
translocates gephyrin to submembrane microaggregates
Title: The GDP-GTP exchange factor collybistin: an essential determinant of neuronal gephyrin clustering.

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General gene information

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Markers

Arhgef9 (e-PCR), detects polymorphism
- UniSTS:536557

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
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	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density	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)

NM_001393743.1 → NP_001380672.1 rho guanine nucleotide exchange factor 9 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021

UniProtKB/TrEMBL

A6IQ19

Related

ENSRNOP00000108703.1, ENSRNOT00000131630.1

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
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, ENSRNOT00000063861.5

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

NC_086039.1 Reference GRCr8

Range

63929168..64087267 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_039100041.1 → XP_038955969.1 rho guanine nucleotide exchange factor 9 isoform X6

UniProtKB/TrEMBL

A6IQ21

Related

ENSRNOP00000111082.1, ENSRNOT00000129280.1

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

UniProtKB/TrEMBL

A0A8I5ZMR8, A6IQ19

Related

ENSRNOP00000099705.1, ENSRNOT00000164841.1

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
XM_063280289.1 → XP_063136359.1 rho guanine nucleotide exchange factor 9 isoform X4
XM_063280288.1 → XP_063136358.1 rho guanine nucleotide exchange factor 9 isoform X4
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
XM_039100040.2 → XP_038955968.1 rho guanine nucleotide exchange factor 9 isoform X5

UniProtKB/TrEMBL

A6IQ22

Related

ENSRNOP00000084571.2, ENSRNOT00000084678.3

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