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O43307 (ARHG9_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 113. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Rho guanine nucleotide exchange factor 9
Alternative name(s):
Collybistin
PEM-2 homolog
Rac/Cdc42 guanine nucleotide exchange factor 9
Gene names
Name:ARHGEF9
Synonyms:ARHDH9, KIAA0424
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length516 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Acts as guanine nucleotide exchange factor (GEF) for CDC42. Promotes formation of GPHN clusters. Ref.5

Subunit structure

Interacts with GPHN.

Subcellular location

Cytoplasm Ref.5.

Tissue specificity

Detected in brain. Detected at low levels in heart. Ref.5

Involvement in disease

Epileptic encephalopathy, early infantile, 8 (EIEE8) [MIM:300607]: A disorder characterized by hyperekplexia and early infantile epileptic encephalopathy. Neurologic features include exaggerated startle response, seizures, impaired psychomotor development, and mental retardation. Seizures can be provoked by tactile stimulation or extreme emotion.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.7

Sequence similarities

Contains 1 DH (DBL-homology) domain.

Contains 1 PH domain.

Contains 1 SH3 domain.

Sequence caution

The sequence BAA24854.2 differs from that shown. Reason: Erroneous initiation.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O43307-1)

Also known as: CB3(SH3+);

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: O43307-2)

Also known as: CB3(SH3-);

The sequence of this isoform differs from the canonical sequence as follows:
     1-10: MTLLITGDSI → MQWIRGGSGM
     11-63: Missing.
Isoform 3 (identifier: O43307-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-102: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 516516Rho guanine nucleotide exchange factor 9
PRO_0000253895

Regions

Domain8 – 6760SH3
Domain103 – 287185DH
Domain318 – 425108PH
Region100 – 11011Interaction with GPHN By similarity

Natural variations

Alternative sequence1 – 102102Missing in isoform 3.
VSP_044555
Alternative sequence1 – 1010MTLLITGDSI → MQWIRGGSGM in isoform 2.
VSP_042920
Alternative sequence11 – 6353Missing in isoform 2.
VSP_042921
Natural variant551G → A in EIEE8; affects dendritic gephrin clustering and trafficking of GABA-A receptors to synapses. Ref.7
VAR_028752
Natural variant4011E → K Probable disease-associated mutation found in a patient with moderate mental retardation, speech delay and sleep disturbances. Ref.8
VAR_069370

Experimental info

Sequence conflict1091N → D in BAF82682. Ref.2

Secondary structure

............. 516
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (CB3(SH3+)) [UniParc].

Last modified October 17, 2006. Version 3.
Checksum: AAEE17366B46B707

FASTA51660,982
        10         20         30         40         50         60 
MTLLITGDSI VSAEAVWDHV TMANRELAFK AGDVIKVLDA SNKDWWWGQI DDEEGWFPAS 

        70         80         90        100        110        120 
FVRLWVNQED EVEEGPSDVQ NGHLDPNSDC LCLGRPLQNR DQMRANVINE IMSTERHYIK 

       130        140        150        160        170        180 
HLKDICEGYL KQCRKRRDMF SDEQLKVIFG NIEDIYRFQM GFVRDLEKQY NNDDPHLSEI 

       190        200        210        220        230        240 
GPCFLEHQDG FWIYSEYCNN HLDACMELSK LMKDSRYQHF FEACRLLQQM IDIAIDGFLL 

       250        260        270        280        290        300 
TPVQKICKYP LQLAELLKYT AQDHSDYRYV AAALAVMRNV TQQINERKRR LENIDKIAQW 

       310        320        330        340        350        360 
QASVLDWEGE DILDRSSELI YTGEMAWIYQ PYGRNQQRVF FLFDHQMVLC KKDLIRRDIL 

       370        380        390        400        410        420 
YYKGRIDMDK YEVVDIEDGR DDDFNVSMKN AFKLHNKETE EIHLFFAKKL EEKIRWLRAF 

       430        440        450        460        470        480 
REERKMVQED EKIGFEISEN QKRQAAMTVR KVPKQKGVNS ARSVPPSYPP PQDPLNHGQY 

       490        500        510 
LVPDGIAQSQ VFEFTEPKRS QSPFWQNFSR LTPFKK 

« Hide

Isoform 2 (CB3(SH3-)) [UniParc].

Checksum: 046F5EC27274EC71
Show »

FASTA46354,965
Isoform 3 [UniParc].

Checksum: 65A0F069D8E0A009
Show »

FASTA41449,458

References

« Hide 'large scale' references
[1]"Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro."
Ishikawa K., Nagase T., Nakajima D., Seki N., Ohira M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
DNA Res. 4:307-313(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Brain.
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
Tissue: Brain and Hippocampus.
[3]"The DNA sequence of the human X chromosome."
Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C. expand/collapse author list , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
Tissue: Brain and Uterus.
[5]"Identification and characterization of hPEM-2, a guanine nucleotide exchange factor specific for Cdc42."
Reid T., Bathoorn A., Ahmadian M.R., Collard J.G.
J. Biol. Chem. 274:33587-33593(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
[6]"Solution structure of the SH3 domain from Rho guanine nucleotide exchange factor 9."
RIKEN structural genomics initiative (RSGI)
Submitted (FEB-2009) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 7-75.
[7]"The GDP-GTP exchange factor collybistin: an essential determinant of neuronal gephyrin clustering."
Harvey K., Duguid I.C., Alldred M.J., Beatty S.E., Ward H., Keep N.H., Lingenfelter S.E., Pearce B.R., Lundgren J., Owen M.J., Smart T.G., Luescher B., Rees M.I., Harvey R.J.
J. Neurosci. 24:5816-5826(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT EIEE8 ALA-55, CHARACTERIZATION OF VARIANT EIEE8 ALA-55, ALTERNATIVE SPLICING.
[8]"Diagnostic exome sequencing in persons with severe intellectual disability."
de Ligt J., Willemsen M.H., van Bon B.W., Kleefstra T., Yntema H.G., Kroes T., Vulto-van Silfhout A.T., Koolen D.A., de Vries P., Gilissen C., del Rosario M., Hoischen A., Scheffer H., de Vries B.B., Brunner H.G., Veltman J.A., Vissers L.E.
N. Engl. J. Med. 367:1921-1929(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT LYS-401.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB007884 mRNA. Translation: BAA24854.2. Different initiation.
AK289993 mRNA. Translation: BAF82682.1.
AK295033 mRNA. Translation: BAG58088.1.
AL451106, AL355142, AL391277 Genomic DNA. Translation: CAI39550.1.
AL391277, AL355142, AL451106 Genomic DNA. Translation: CAI40401.1.
AL355142, AL391277, AL451106 Genomic DNA. Translation: CAI41195.1.
BC056892 mRNA. No translation available.
BC117406 mRNA. Translation: AAI17407.1.
CCDSCCDS35315.1. [O43307-1]
CCDS55429.1. [O43307-3]
CCDS55430.1. [O43307-2]
RefSeqNP_001166950.1. NM_001173479.1. [O43307-2]
NP_001166951.1. NM_001173480.1. [O43307-3]
NP_056000.1. NM_015185.2. [O43307-1]
UniGeneHs.54697.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2YSQNMR-A7-75[»]
ProteinModelPortalO43307.
SMRO43307. Positions 4-450.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116834. 5 interactions.
IntActO43307. 1 interaction.
STRING9606.ENSP00000253401.

PTM databases

PhosphoSiteO43307.

Proteomic databases

PaxDbO43307.
PRIDEO43307.

Protocols and materials databases

DNASU23229.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000253401; ENSP00000253401; ENSG00000131089. [O43307-1]
ENST00000374870; ENSP00000364004; ENSG00000131089. [O43307-3]
ENST00000437457; ENSP00000399994; ENSG00000131089. [O43307-2]
ENST00000601443; ENSP00000469587; ENSG00000268229. [O43307-1]
ENST00000601864; ENSP00000471377; ENSG00000268229. [O43307-2]
ENST00000602267; ENSP00000469767; ENSG00000268229. [O43307-3]
GeneID23229.
KEGGhsa:23229.
UCSCuc004dvj.2. human. [O43307-1]
uc011mot.2. human. [O43307-2]

Organism-specific databases

CTD23229.
GeneCardsGC0XM062771.
GeneReviewsARHGEF9.
HGNCHGNC:14561. ARHGEF9.
HPAHPA035419.
MIM300429. gene.
300607. phenotype.
neXtProtNX_O43307.
Orphanet163985. Hyperekplexia - epilepsy.
PharmGKBPA24978.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5422.
HOGENOMHOG000237363.
HOVERGENHBG050568.
OMAKVTKQKG.
PhylomeDBO43307.
TreeFamTF316832.

Enzyme and pathway databases

ReactomeREACT_111102. Signal Transduction.
REACT_13685. Neuronal System.
REACT_15518. Transmembrane transport of small molecules.

Gene expression databases

ArrayExpressO43307.
BgeeO43307.
CleanExHS_ARHGEF9.
GenevestigatorO43307.

Family and domain databases

Gene3D1.20.900.10. 1 hit.
2.30.29.30. 1 hit.
InterProIPR000219. DH-domain.
IPR011993. PH_like_dom.
IPR001849. Pleckstrin_homology.
IPR001452. SH3_domain.
[Graphical view]
PfamPF00169. PH. 1 hit.
PF00621. RhoGEF. 1 hit.
PF14604. SH3_9. 1 hit.
[Graphical view]
SMARTSM00233. PH. 1 hit.
SM00325. RhoGEF. 1 hit.
SM00326. SH3. 1 hit.
[Graphical view]
SUPFAMSSF48065. SSF48065. 1 hit.
SSF50044. SSF50044. 1 hit.
PROSITEPS50010. DH_2. 1 hit.
PS50003. PH_DOMAIN. 1 hit.
PS50002. SH3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO43307.
GeneWikiARHGEF9.
GenomeRNAi23229.
NextBio44841.
PROO43307.
SOURCESearch...

Entry information

Entry nameARHG9_HUMAN
AccessionPrimary (citable) accession number: O43307
Secondary accession number(s): A8K1S8 expand/collapse secondary AC list , B4DHC7, F8W7P8, Q5JSL6
Entry history
Integrated into UniProtKB/Swiss-Prot: October 17, 2006
Last sequence update: October 17, 2006
Last modified: July 9, 2014
This is version 113 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome X

Human chromosome X: entries, gene names and cross-references to MIM