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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ARHGEF39 Gene

protein-coding   GIFtS: 41
GCID: GC09M035658

Rho Guanine Nucleotide Exchange Factor (GEF) 39

(Previous name: chromosome 9 open reading frame 100)
(Previous symbol: C9orf100)
  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Rho Guanine Nucleotide Exchange Factor (GEF) 391 2
C9orf1001 2 3
Chromosome 9 Open Reading Frame 1001
RP11-331F9.72
Rho Guanine Nucleotide Exchange Factor 392
Vav-Like Protein C9orf1002

External Ids:    HGNC: 259091   Entrez Gene: 849042   Ensembl: ENSG000001371357   UniProtKB: Q8N4T43   

Export aliases for ARHGEF39 gene to outside databases


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for ARHGEF39 Gene: 
ARHGEF39 (Rho guanine nucleotide exchange factor (GEF) 39) is a protein-coding gene. Diseases associated with ARHGEF39 include hepatocellular carcinoma. GO annotations related to this gene include phospholipid binding and Rho guanyl-nucleotide exchange factor activity.

UniProtKB/Swiss-Prot: ARG39_HUMAN, Q8N4T4
Function: Promotes cell proliferation




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000009.11  NT_008413.18  NC_018920.2  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for ARHGEF39
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): ARHGEF39 promoter sequence
   Search SABiosciences Chromatin IP Primers for ARHGEF39

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ARHGEF39


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 9p13.3   Ensembl cytogenetic band:  9p13.3   HGNC cytogenetic band: 9p13.3

ARHGEF39 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ARHGEF39 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M035658:  view genomic region     (about GC identifiers)

Start:
35,658,872 bp from pter      End:
35,675,863 bp from pter
Size:
16,992 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: ARG39_HUMAN, Q8N4T4 (See protein sequence)
Recommended Name: Rho guanine nucleotide exchange factor 39  
Size: 335 amino acids; 38295 Da
Subcellular location: Cell membrane
Sequence caution: Sequence=AAR01010.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=AAR01011.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: Q49AG0 Q6TPQ2 Q96ST6
Alternative splicing: 4 isoforms:  Q8N4T4-1   Q8N4T4-2   Q8N4T4-3   Q8N4T4-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ARHGEF39: NX_Q8N4T4

Explore proteomics data for ARHGEF39 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8N4T4

  • ARHGEF39 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    ARHGEF39 Protein Expression
    REFSEQ proteins: NP_116207.2  
    ENSEMBL proteins: 
     ENSP00000436756   ENSP00000436519   ENSP00000367638   ENSP00000367648   ENSP00000344922  

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    Novus Biologicals ARHGEF39 Lysates
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    Browse Sino Biological Cell Lysates 
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    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005886plasma membrane IDA--

    ARHGEF39 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    3 InterPro protein domains:
     IPR000219 DH-domain
     IPR001849 Pleckstrin_homology
     IPR011993 PH_like_dom

    Graphical View of Domain Structure for InterPro Entry Q8N4T4

    ProtoNet protein and cluster: Q8N4T4

    2 Blocks protein domains:
    IPB000219 DH domain
    IPB001849 Pleckstrin-like


    UniProtKB/Swiss-Prot: ARG39_HUMAN, Q8N4T4
    Similarity: Contains 1 DH (DBL-homology) domain
    Similarity: Contains 1 PH domain


    ARHGEF39 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ARG39_HUMAN, Q8N4T4
    Function: Promotes cell proliferation

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005089Rho guanyl-nucleotide exchange factor activity IEA--
    GO:0005515protein binding ----
    GO:0005543phospholipid binding IEA--
         
    ARHGEF39 for ontologies           About GeneDecksing


    Animal Models:
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    Inhib. RNA
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ARHGEF39

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    4 Interacting proteins for ARHGEF39 (Q8N4T42, 3 ENSP000003676384) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RBPMSQ930622, 3, ENSP000003401764MINT-66846 I2D: score=5 STRING: ENSP00000340176
    DVL2O146412, 3, ENSP000000053404MINT-66662 I2D: score=5 STRING: ENSP00000005340
    HAX1O001653I2D: score=1 
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030335positive regulation of cell migration IDA--
    GO:0035023regulation of Rho protein signal transduction IEA--

    ARHGEF39 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for ARHGEF39 (ARG39)

    Search CenterWatch for drugs/clinical trials and news about ARHGEF39 / ARG39

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for ARHGEF39 gene: 
    NM_032818.2  

    Unigene Cluster for ARHGEF39:

    Rho guanine nucleotide exchange factor (GEF) 39
    Hs.534579  [show with all ESTs]
    Unigene Representative Sequence: NM_032818
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000490638(uc003zxl.3) ENST00000475323 ENST00000378387(uc003zxm.1 uc011loz.1)
    ENST00000490970 ENST00000488918 ENST00000468876 ENST00000378395 ENST00000343259

    miRNA
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    Inhib. RNA
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat ARHGEF39
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    Additional mRNA sequence: 

    AK001187.1 AK225501.1 AK225529.1 AK303513.1 BC033666.1 

    13 DOTS entries:

    DT.92417363  DT.101983915  DT.445862  DT.100755207  DT.100751488  DT.101983914  DT.97845312  DT.121152905 
    DT.121152875  DT.91735220  DT.121152882  DT.91995466  DT.92027373 

    24/158 AceView cDNA sequences (see all 158):

    BM680405 BC033666 CA488943 BF796667 AA421195 BE561205 AA235662 CR624155 
    BQ057760 AA356801 BQ054614 NM_014450 CR617531 AW674851 AW404968 AA380418 
    BE018581 AY390226 AA459295 AA827647 AA430511 AY390225 AA746595 AI821531 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for ARHGEF39 (see all 7)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b
    SP1:                                -                 -                                                   
    SP2:                                -                 -                                                   
    SP3:                    -           -                 -     -     -                                       
    SP4:                                -                                                                     
    SP5:                                                        -     -     -     -     -                     


    ECgene alternative splicing isoforms for ARHGEF39

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section
    See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: --


    ARHGEF39 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/2 selected tissues (see all 2) fully expand
     
     Thymus (Hematopoietic System)
             Double Positive Thymocytes Thymus
     
     Blood (Cardiovascular System)
             Double Positive Thymocytes Thymus

    See ARHGEF39 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ARHGEF39

    SOURCE GeneReport for Unigene cluster: Hs.534579

    UniProtKB/Swiss-Prot: ARG39_HUMAN, Q8N4T4
    Tissue specificity: Strongly expressed in hepatocellular carcinoma (HCC) compared with their non-cancerous
    counterparts

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for ARHGEF39 gene from 5/12 species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Arhgef391 , 5 RIKEN cDNA E130306D19 gene5
    Rho guanine nucleotide exchange factor (GEF) 391
    85.47(n)1
    86.57(a)1
      4 (23.04 cM)5
    2300981  NM_001013377.21  NP_001013395.21 
     434961425 
    chicken
    (Gallus gallus)
    Aves CZH9orf1001 chromosome Z open reading frame, human C9orf100 61.18(n)
    57.45(a)
      431661  NM_001195689.1  NP_001182618.1 
    lizard
    (Anolis carolinensis)
    Reptilia ARHGEF396
    Uncharacterized protein
    48(a)
    1 ↔ 1
    GL343859.1(87408-97455)
    zebrafish
    (Danio rerio)
    Actinopterygii arhgef391 Rho guanine nucleotide exchange factor (GEF) 39 56.43(n)
    50.15(a)
      492469  NM_001007341.1  NP_001007342.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta RhoGEF41 CG8606-PA 43.38(n)
    26.47(a)
      38806  NM_139844.2  NP_648101.1 


    ENSEMBL Gene Tree for ARHGEF39 (if available)
    TreeFam Gene Tree for ARHGEF39 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/128 SNPs in ARHGEF39 are shown (see all 128)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1911893241,2
    --35662125(+) ATTTCC/TTGCTT 1 -- int10--------
    rs1837469191,2
    C--35662144(+) CATCAC/TAGCAC 1 -- int10--------
    rs1884161931,2
    C--35662157(+) TTCCTA/GGGGGA 1 -- int10--------
    rs1927485791,2
    C--35662161(+) TGGGGA/GAAGAC 1 -- int10--------
    rs2013883881,2
    --35662199(+) CTGTGA/GTACCA 2 Y syn10--------
    rs1451024141,2
    C,F--35662207(+) CCAGCG/ATGACA 2 /R /C mis11Minor allele frequency- A:0.00NA 4550
    rs1467444381,2
    C--35662214(+) GACAGC/ATCCTC 2 /E /D mis11Minor allele frequency- A:0.00NA 4550
    rs22978791,2,4
    C,F,H--35662251(-) CCCTCA/GTGAGA 2 H R mis1 ese327Minor allele frequency- G:0.31EA NS NA WA EU 10127
    rs1900345411,2
    --35662495(+) GTTCCC/TACCTA 1 -- int10--------
    rs1404232311,2
    C--35662497(+) TCCCAC/TCTATT 1 -- int10--------

    HapMap Linkage Disequilibrium report for ARHGEF39 (35658872 - 35675863 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for ARHGEF39: --
    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    2 diseases for ARHGEF39:    About MalaCards
    hepatocellular carcinoma    


    ARHGEF39 for disorders           About GeneDecksing


    Export disorders for ARHGEF39 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for ARHGEF39 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with ARHGEF39)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. C9orf100, a new member of the Dbl-family guanine nucle otide exchange factors, promotes cell proliferation and migration in hepatocellu lar carcinoma. (PubMed id 22327280)1, 2, 3 Wang H....Cai B. (2012)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    4. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    5. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    6. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    7. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (2005)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    9. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (2004)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 84904 HGNC: 25909 AceView: SITandC9orf100 Ensembl:ENSG00000137135 euGenes: HUgn84904
    ECgene: ARHGEF39 H-InvDB: ARHGEF39

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for ARHGEF39 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for ARHGEF39 gene:
    Search GeneIP for patents involving ARHGEF39

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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