LOCUS       NM_001353921            4702 bp    mRNA    linear   PRI 11-OCT-2024
DEFINITION  Homo sapiens Cdc42 guanine nucleotide exchange factor 9 (ARHGEF9),
            transcript variant 5, mRNA.
ACCESSION   NM_001353921 XM_005262249
VERSION     NM_001353921.2
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 4702)
  AUTHORS   Ma,X., Yan,W., Xu,P., Ma,L., Zan,Y., Huang,L., Wang,G., Liu,L. and
            Hui,W.
  TITLE     LncRNA-p21 suppresses cell proliferation and induces apoptosis in
            gastric cancer by sponging miR-514b-3p and up-regulating ARHGEF9
            expression
  JOURNAL   Biol Chem 403 (10), 945-958 (2022)
   PUBMED   35947460
  REMARK    GeneRIF: LncRNA-p21 suppresses cell proliferation and induces
            apoptosis in gastric cancer by sponging miR-514b-3p and
            up-regulating ARHGEF9 expression.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4702)
  AUTHORS   Yang,H., Liao,H., Gan,S., Xiao,T. and Wu,L.
  TITLE     ARHGEF9 gene variant leads to developmental and epileptic
            encephalopathy: Genotypic phenotype analysis and treatment
            exploration
  JOURNAL   Mol Genet Genomic Med 10 (7), e1967 (2022)
   PUBMED   35638461
  REMARK    GeneRIF: ARHGEF9 gene variant leads to developmental and epileptic
            encephalopathy: Genotypic phenotype analysis and treatment
            exploration.
REFERENCE   3  (bases 1 to 4702)
  AUTHORS   Hines,D.J., Contreras,A., Garcia,B., Barker,J.S., Boren,A.J.,
            Moufawad El Achkar,C., Moss,S.J. and Hines,R.M.
  TITLE     Human ARHGEF9 intellectual disability syndrome is phenocopied by a
            mutation that disrupts collybistin binding to the GABAA receptor
            alpha2 subunit
  JOURNAL   Mol Psychiatry 27 (3), 1729-1741 (2022)
   PUBMED   35169261
  REMARK    GeneRIF: Human ARHGEF9 intellectual disability syndrome is
            phenocopied by a mutation that disrupts collybistin binding to the
            GABAA receptor alpha2 subunit.
REFERENCE   4  (bases 1 to 4702)
  AUTHORS   Ghesh,L., Besnard,T., Nizon,M., Trochu,E., Landeau-Trottier,G.,
            Breheret,F., Thauvin-Robinet,C., Bruel,A.L., Kuentz,P., Coubes,C.,
            Cuisset,L., Mignot,C., Keren,B., Bezieau,S. and Cogne,B.
  TITLE     Loss-of-function variants in ARHGEF9 are associated with an
            X-linked intellectual disability dominant disorder
  JOURNAL   Hum Mutat 42 (5), 498-505 (2021)
   PUBMED   33600053
  REMARK    GeneRIF: Loss-of-function variants in ARHGEF9 are associated with
            an X-linked intellectual disability dominant disorder.
REFERENCE   5  (bases 1 to 4702)
  AUTHORS   Scala,M., Zonneveld-Huijssoon,E., Brienza,M., Mecarelli,O., van der
            Hout,A.H., Zambrelli,E., Turner,K., Zara,F., Peron,A., Vignoli,A.
            and Striano,P.
  TITLE     De novo ARHGEF9 missense variants associated with
            neurodevelopmental disorder in females: expanding the genotypic and
            phenotypic spectrum of ARHGEF9 disease in females
  JOURNAL   Neurogenetics 22 (1), 87-94 (2021)
   PUBMED   32939676
  REMARK    GeneRIF: De novo ARHGEF9 missense variants associated with
            neurodevelopmental disorder in females: expanding the genotypic and
            phenotypic spectrum of ARHGEF9 disease in females.
REFERENCE   6  (bases 1 to 4702)
  AUTHORS   Harrington,A.W., Kim,J.Y. and Yoon,S.O.
  TITLE     Activation of Rac GTPase by p75 is necessary for c-jun N-terminal
            kinase-mediated apoptosis
  JOURNAL   J Neurosci 22 (1), 156-166 (2002)
   PUBMED   11756498
REFERENCE   7  (bases 1 to 4702)
  AUTHORS   Grosskreutz,Y., Hermann,A., Kins,S., Fuhrmann,J.C., Betz,H. and
            Kneussel,M.
  TITLE     Identification of a gephyrin-binding motif in the GDP/GTP exchange
            factor collybistin
  JOURNAL   Biol Chem 382 (10), 1455-1462 (2001)
   PUBMED   11727829
  REMARK    GeneRIF: Here we identified residues critical for interaction with
            gephyrin in the linker region between the SH3 and the DH domains of
            collybistin.
REFERENCE   8  (bases 1 to 4702)
  AUTHORS   Kins,S., Betz,H. and Kirsch,J.
  TITLE     Collybistin, a newly identified brain-specific GEF, induces
            submembrane clustering of gephyrin
  JOURNAL   Nat Neurosci 3 (1), 22-29 (2000)
   PUBMED   10607391
REFERENCE   9  (bases 1 to 4702)
  AUTHORS   Reid,T., Bathoorn,A., Ahmadian,M.R. and Collard,J.G.
  TITLE     Identification and characterization of hPEM-2, a guanine nucleotide
            exchange factor specific for Cdc42
  JOURNAL   J Biol Chem 274 (47), 33587-33593 (1999)
   PUBMED   10559246
REFERENCE   10 (bases 1 to 4702)
  AUTHORS   Balint,B. and Thomas,R.
  TITLE     Hereditary Hyperekplexia Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301437
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL451106.9, AL355142.11 and
            AL391277.16.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Jun 2, 2019 this sequence version replaced NM_001353921.1.
            
            Summary: The protein encoded by this gene is a Rho-like GTPase that
            switches between the active (GTP-bound) state and inactive
            (GDP-bound) state to regulate CDC42 and other genes. This
            brain-specific protein also acts as an adaptor protein for the
            recruitment of gephyrin and together these proteins facilitate
            receceptor recruitement in GABAnergic and glycinergic synapses.
            Defects in this gene are the cause of startle disease with epilepsy
            (STHEE), also known as hyperekplexia with epilepsy, as well as
            several other types of cognitive disability. Multiple transcript
            variants encoding different isoforms have been found for this gene.
            [provided by RefSeq, Jul 2017].
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660803.73044.1,
                                           SRR1660803.36637.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000671741.2/ ENSP00000500715.1
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-99                AL451106.9         45603-45701         c
            100-279             AL355142.11        41494-41673         c
            280-471             AL355142.11        23220-23411         c
            472-651             AL355142.11        14087-14266         c
            652-884             AL391277.16        189658-189890       c
            885-1014            AL391277.16        185356-185485       c
            1015-1146           AL391277.16        177204-177335       c
            1147-1390           AL391277.16        166812-167055       c
            1391-1459           AL391277.16        155298-155366       c
            1460-4702           AL391277.16        146285-149527       c
FEATURES             Location/Qualifiers
     source          1..4702
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xq11.1"
     gene            1..4702
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /note="Cdc42 guanine nucleotide exchange factor 9"
                     /db_xref="GeneID:23229"
                     /db_xref="HGNC:HGNC:14561"
                     /db_xref="MIM:300429"
     exon            1..99
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /inference="alignment:Splign:2.1.0"
     CDS             70..1641
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /note="isoform 5 is encoded by transcript variant 5;
                     hPEM-2 collybistin; rho guanine nucleotide exchange factor
                     9; PEM-2 homolog; rac/Cdc42 guanine nucleotide exchange
                     factor 9; Cdc42 guanine nucleotide exchange factor (GEF)
                     9"
                     /codon_start=1
                     /product="rho guanine nucleotide exchange factor 9 isoform
                     5"
                     /protein_id="NP_001340850.1"
                     /db_xref="CCDS:CCDS94619.1"
                     /db_xref="GeneID:23229"
                     /db_xref="HGNC:HGNC:14561"
                     /db_xref="MIM:300429"
                     /translation="MQWIRGGSGMLITGDSIVSAEAVWDHVTMANRELAFKAGDVIKV
                     LDASNKDWWWGQIDDEEGWFPASFVRLWVNQEDEVEEGPSDVQNGHLDPNSDCLCLGR
                     PLQNRDQMRANVINEIMSTERHYIKHLKDICEGYLKQCRKRRDMFSDEQLKVIFGNIE
                     DIYRFQMGFVRDLEKQYNNDDPHLSEIGPCFLEHQDGFWIYSEYCNNHLDACMELSKL
                     MKDSRYQHFFEACRLLQQMIDIAIDGFLLTPVQKICKYPLQLAELLKYTAQDHSDYRY
                     VAAALAVMRNVTQQINERKRRLENIDKIAQWQASVLDWEGEDILDRSSELIYTGEMAW
                     IYQPYGRNQQRVFFLFDHQMVLCKKDLIRRDILYYKGRIDMDKYEVVDIEDGRDDDFN
                     VSMKNAFKLHNKETEEIHLFFAKKLEEKIRWLRAFREERKMVQEDEKIGFEISENQKR
                     QAAMTVRKVPKQKGVNSARSVPPSYPPPQDPLNHGQYLVPDGIAQSQVFEFTEPKRSQ
                     SPFWQNFSRLTPFKK"
     exon            100..279
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /inference="alignment:Splign:2.1.0"
     exon            280..471
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /inference="alignment:Splign:2.1.0"
     exon            472..651
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /inference="alignment:Splign:2.1.0"
     exon            652..884
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /inference="alignment:Splign:2.1.0"
     exon            885..1014
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /inference="alignment:Splign:2.1.0"
     exon            1015..1146
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /inference="alignment:Splign:2.1.0"
     exon            1147..1390
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /inference="alignment:Splign:2.1.0"
     exon            1391..1459
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /inference="alignment:Splign:2.1.0"
     exon            1460..4702
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4682..4687
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /note="hexamer: AATAAA"
     polyA_site      4702
                     /gene="ARHGEF9"
                     /gene_synonym="COLLYBISTIN; DEE8; EIEE8; HPEM-2; PEM-2;
                     PEM2"
                     /note="major polyA site"
ORIGIN      
        1 ccttctagtc agcccgcgac aactcgcgcc agctacgggg cctcagagaa gccggacttc
       61 gcaagcacca tgcagtggat aaggggcgga tcgggaatgc tgatcactgg agattccatc
      121 gttagtgctg aggcagtatg ggatcacgtc accatggcca accgggagtt ggcatttaaa
      181 gctggcgacg tcatcaaagt cttggatgct tccaacaagg attggtggtg gggccagatc
      241 gacgatgagg agggatggtt tcctgccagc tttgtgaggc tctgggtgaa ccaggaggat
      301 gaggtggagg aggggcccag cgatgtgcag aacggacacc tggaccccaa ttcagactgc
      361 ctctgtctgg ggcggccact acagaaccgg gaccagatgc gggccaatgt catcaatgag
      421 ataatgagca ctgagcgtca ctacatcaag cacctcaagg atatttgtga gggctatctg
      481 aagcagtgcc ggaagagaag ggacatgttc agtgacgagc aactgaaggt aatctttggg
      541 aacattgaag atatctacag atttcagatg ggctttgtga gagacctgga gaaacagtat
      601 aacaatgatg acccccacct cagcgagata ggaccctgct tcctagagca ccaagatgga
      661 ttctggatat actctgagta ttgtaacaac cacctggatg cttgcatgga gctctccaaa
      721 ctgatgaagg acagccgcta ccagcacttc tttgaggcct gtcgcctctt gcagcagatg
      781 attgacattg ctatcgatgg tttccttttg actccagtgc agaagatctg caagtatccc
      841 ttacagttgg ctgagctcct aaagtatact gcccaagacc acagtgacta caggtatgtg
      901 gcagctgctt tggctgtcat gagaaatgtg actcagcaga tcaacgaacg caagcgacgt
      961 ttagagaata ttgacaagat tgctcagtgg caggcttctg tcctagactg ggagggcgag
     1021 gacatcctag acaggagctc ggagctgatc tacactgggg agatggcctg gatctaccag
     1081 ccctacggcc gcaaccagca gcgggtcttc ttcctgtttg accaccagat ggtcctctgc
     1141 aagaaggacc taatccggag agacatcctg tactacaaag gccgcattga catggataaa
     1201 tatgaggtag ttgacattga ggatggcaga gatgatgact tcaatgtcag catgaagaat
     1261 gcctttaagc ttcacaacaa ggagactgag gagatacatc tgttctttgc caagaagctg
     1321 gaggaaaaaa tacgctggct cagggctttc agagaagaga ggaaaatggt acaggaagat
     1381 gaaaaaattg gctttgaaat ttctgaaaac cagaagaggc aggctgcaat gactgtgaga
     1441 aaagtcccta agcaaaaagg tgtcaactct gcccgctcag ttcctccttc ctacccacca
     1501 ccgcaggacc cgttaaacca cggccagtac ctggtccccg acggcatcgc tcagtcgcag
     1561 gtctttgagt tcaccgaacc caagcgcagc cagtcaccat tctggcaaaa cttcagcagg
     1621 ttaaccccct tcaaaaaatg atacctacag ggaggcagat aattttaaaa taaagtaaat
     1681 aaaattatat ttatagatgg accttttttc ggagaagcac tgttgaaatt tatacacaca
     1741 cacacacaca gagacccttg agtacacata cacacacaca cacacagaca cacacacaca
     1801 cacacacaca cacacacaca cagagagata aggaacaaaa gtgttttctg ttgttttggg
     1861 gaagtgaaat atgtggttgg taggaagagg taccaatgac ttccaaacat gtgattccgt
     1921 cttaaaagtt ttccattttt accctgtccc ccttcccttt gctttcagaa gttgacattt
     1981 ctattcattg cttttcttgt taagataatc tctttactcc cctgtgagtg attcactgcc
     2041 ttgtcattat tacgatagat gtgtttgtat tgtttttttt ctgatgatac tgatgttgat
     2101 gaatttttaa ttttatttga tgtggtagag ttgggaggtt tcagggtttt ttcccctctt
     2161 ttactttcca ttgaggaagg gaatgagctc ctttctcctc tccttcagcc aatcattatc
     2221 aaatgttcct tcagccctgc agttgcccca aataaccttt tttcagcatc ctctgtcctc
     2281 agtcatgcca gtctggacat gctctgttgt gccctgtgac aaaactgctc agtattccta
     2341 ttgcttttac tgtgttttag gtactgtgaa gggatcaaaa aaccaaacag aagcaaggga
     2401 gtatcagact atgatgatgc tggagtggac ttctgttcag ggaacatttt gcattcaggc
     2461 tgtttcttct atcactgggg tttcccatgt tgcagcactt ctgggtcgtt gcaattttgc
     2521 atctaggagt tagtttgatc gagttattct cttttttcaa gtcacttttg ttataggtct
     2581 ccccctaggc ctgtctctcc cttagcccaa aagatctgaa ctggaagcag aggttgagat
     2641 tctgcctccc aggagaggga tttacctgcc ccctagtacc agataggttt agggcagtga
     2701 tctctacagc aatcagttca gtgtcctggt tgtccctgct cccatttaca gatgtttggg
     2761 cagcattgat agaagtatgg aggggttcaa gacagagccc acctgatcaa gatcatcagc
     2821 taccttcaaa ttattgacct ggacagggtc caagtctgat agtaaccttt tacaagaaag
     2881 aacagggatg ggaatggaaa gagatagcct tgatccacag tattgtacct gcattttcta
     2941 ccaccctaaa attgtgtgag acttctccca ttgttaacag attgcatgga caatcttccc
     3001 tggcttcttt ctttccctct ctctttcttc tttctcctgc catcctagca caggaggatt
     3061 tttggtattg atatagttaa agctgttctg gcactcaaag aaggccgtgt ttccaacatc
     3121 ctctcatccc aggacatttg gggcaagtga gttaggggcc caggggcaat tttccctctg
     3181 aataacgtgt ctgaggcagg gatgctaccc tcaggctcgc ttttggccag ctttttgctt
     3241 gggaaaatct aacttctttc acaaggaggc aggcttccta tggatgttgg agtacctgtt
     3301 tttcctccac acatagccct tttcatggat agaccttgaa caacaaaaag ggtataaggg
     3361 aataaggatg aactctgctg tgaagagcaa gccactgtag tgaggaatgt ggagactggg
     3421 agtctgtcct aaaccccatg ggagaagact tcatcatgac aggacttcag cttaccaagc
     3481 agcagccata gctgtgtgga ggcttcagca tagctagcat gtttactgct ctatgcctcc
     3541 tgatccagac caggcattgc ccagcctggg aatcttttct ttgtgggaat caaattacaa
     3601 gctatttaag tttatattcc atcacaacca agtcagactt gtattataag tcaaggatga
     3661 gcctgatctg gggagagggc cggggctcgg gactggccac cactgttcag cacatgacct
     3721 aactacgtaa gcctctttgg caagggtcct ggtgcccagc acccaggcta aaatatcctg
     3781 tctggcagag tgttttggta gctatgcagg cctcccttca gtgtacctct ttttccaact
     3841 tctcactcct ccttactagg cttggccttg acatgcttct tcgagggttg gcagcacacc
     3901 gggaggggat gcttggacaa gtttctgggc ctacatttct tgactaggcc ctctcatttc
     3961 ctccctcctt ggggcttctg cccagggctc caggatcagg gatattactt ctcaacccgc
     4021 acttctcctc tactgaaccc actggcatca cctgatgcca ctaatttgtg aacaacaaga
     4081 aatcatttcc ccattggttg gagtattccc tcagcctata gcatcaaagc agaccagtgg
     4141 ccaacagccc caaggggagc ccaattaaat acctgggttc agtatcctaa cctgttatgt
     4201 cctgacagca atggtaaccc cagtaattct gtaatgttgt aatttccgca tggccctgag
     4261 ctcccttttc ctcaactcag tgaggccagg atttgctctc caaaaggctt tgctagtgtg
     4321 ttcaatggga cctgctgtgg ggagtcctaa gacagacatc taattattct ctctttttcc
     4381 ccccctctct atgtgtatat ttctaatgga tctataagaa cagcaacaag agagttctaa
     4441 caattctagt gtgaagccaa atagtgatct tttagtgctt tggggatggg gtgggctggg
     4501 gtggatggat gggcaacagt gactttgatt acccttgctg ctctgcattt gccagtttat
     4561 tcttttgttt cttttatctg actgactctg tcaaacaagt gtcaaagttg tgtgttaaaa
     4621 aatgtttaac aaaaaaaatg ttgtaatgac acaaagcctt atgaaaatat ttatggagtt
     4681 caataaaaga agtaaaaaga ca
//
