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

FGD6 Gene

protein-coding   GIFtS: 49
GCID: GC12M095470

FYVE, RhoGEF and PH domain containing 6
  Search for FGD6
in
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our new
 Human Malady Compendium 
Biological research products
for FGD6    

Aliases
for FGD6 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
FYVE, RhoGEF And PH Domain Containing 61 2
ZFYVE241 2 3
Zinc Finger FYVE Domain-Containing Protein 242 3
FLJ111831
FYVE, RhoGEF And PH Domain-Containing Protein 62
KIAA13623

External Ids:    HGNC: 217401   Entrez Gene: 557852   Ensembl: ENSG000001802637   OMIM: 6135205   UniProtKB: Q6ZV733   

Export aliases for FGD6 gene to outside databases

Previous GC identifers: GC12M093976 GC12M092538


Summaries
for FGD6 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
UniProtKB/Swiss-Prot: FGD6_HUMAN, Q6ZV73
Function: May activate CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for
free GTP. May play a role in regulating the actin cytoskeleton and cell shape (By similarity)




Genomic Views
for FGD6 gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000012.11  NC_018923.1  NT_029419.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the FGD6 gene promoter:
         E2F-3a   E2F-4   E2F-5   Pbx1a   E2F-2   LCR-F1   E2F   E2F-1   FOXJ2 (long isoform)   FOXJ2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: FGD6 promoter sequence
   Search SABiosciences Chromatin IP Primers for FGD6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat FGD6


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

Entrez Gene cytogenetic band: 12q22   Ensembl cytogenetic band:  12q22   HGNC cytogenetic band: 12q23.1

FGD6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FGD6 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M095470:  view genomic region     (about GC identifiers)

Start:
 95,470,525 bp from pter      End:
 95,611,258 bp from pter
Size:
 140,734 bases      Orientation:
 minus strand

Proteins
for FGD6 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: FGD6_HUMAN, Q6ZV73 (See protein sequence)
Recommended Name: FYVE, RhoGEF and PH domain-containing protein 6  
Size: 1430 amino acids; 160816 Da
Subcellular location: Cytoplasm (Probable). Cytoplasm, cytoskeleton (Probable)
Sequence caution: Sequence=BAA92052.1; Type=Erroneous initiation; Sequence=BAA92600.1; Type=Frameshift; Positions=1365;
Sequence=BAC87464.1; Type=Erroneous initiation; Sequence=CAD98096.1; Type=Miscellaneous discrepancy;
Note=Contaminating sequence. Potential poly-A sequence;
Secondary accessions: Q6ZR53 Q7Z2Z7 Q96D44 Q9NUR8 Q9P2I5
Alternative splicing: 2 isoforms:  Q6ZV73-1   Q6ZV73-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for FGD6: NX_Q6ZV73

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q6ZV73

    • FGD6 Protein expression data from MOPED and PaxDb:    About this image 
    FGD6 Protein Expression
    REFSEQ proteins: NP_060821.3  
    ENSEMBL proteins: 
     ENSP00000344446   ENSP00000448350   ENSP00000408291   ENSP00000450342   ENSP00000450240  
     ENSP00000449005  

    Human Recombinant Protein Products for FGD6: 
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    Uscn Proteins for FGD6

    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001726ruffle ISS--
    GO:0005622intracellular ----
    GO:0005737cytoplasm ISS--
    GO:0005794Golgi apparatus ISS--
    GO:0005856cytoskeleton IEA--

    FGD6 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for FGD6 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    FGD6 for domains           About GeneDecksing

    5/6 InterPro domains/families (see all 6):
     IPR000219 DH-domain
     IPR001849 Pleckstrin_homology
     IPR000306 Znf_FYVE
     IPR011993 PH_like_dom
     IPR013083 Znf_RING/FYVE/PHD

    Graphical View of Domain Structure for InterPro Entry Q6ZV73

    ProtoNet protein and cluster: Q6ZV73

    3 Blocks protein families:
    IPB000219 DH domain
    IPB000306 Zn-finger
    IPB001849 Pleckstrin-like


    UniProtKB/Swiss-Prot: FGD6_HUMAN, Q6ZV73
    Similarity: Contains 1 DH (DBL-homology) domain
    Similarity: Contains 1 FYVE-type zinc finger
    Similarity: Contains 2 PH domains


    Function
    for FGD6 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, 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, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Molecular Function:

         UniProtKB/Swiss-Prot Summary: FGD6_HUMAN, Q6ZV73
    Function: May activate CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for
    free GTP. May play a role in regulating the actin cytoskeleton and cell shape (By similarity)

         Gene Ontology (GO): 5 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005085guanyl-nucleotide exchange factor activity ISS--
    GO:0005089Rho guanyl-nucleotide exchange factor activity IEA--
    GO:0005543phospholipid binding IEA--
    GO:0031267small GTPase binding ISS--
    GO:0046872metal ion binding IEA--
         
    FGD6 for ontologies           About GeneDecksing


    Phenotypes:
         3 GenomeRNAi human phenotypes for FGD6:
     Decreased Tat-dependent transc  Decreased p24 protein expressi  Synthetic lethal with c-Myc af 

    Animal Models:
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for FGD6 

    miRNA
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    hsa-miR-193a-3p hsa-miR-128 hsa-miR-30d hsa-miR-519a hsa-miR-30a hsa-miR-3613-3p hsa-miR-155* hsa-miR-761
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    Gene Editing
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    In Situ Assay
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    Pathways & Interactions
    for FGD6 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for FGD6

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

    5/6 Interacting proteins for FGD6 (Q6ZV733 ENSP000003444464) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ACVR1Q047713, ENSP000002636404I2D: score=2 STRING: ENSP00000263640
    YWHAGP619813, ENSP000003063304I2D: score=1 STRING: ENSP00000306330
    AXIN2Q9Y2T13I2D: score=1 
    DVL2O146413I2D: score=1 
    NKD1Q969G93I2D: score=1 
    About this table

    Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007010cytoskeleton organization ISS--
    GO:0008360regulation of cell shape ISS--
    GO:0030036actin cytoskeleton organization ISS--
    GO:0035023regulation of Rho protein signal transduction ----
    GO:0043088regulation of Cdc42 GTPase activity ISS--

    FGD6 for ontologies           About GeneDecksing



    Drugs & Compounds
    for FGD6 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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
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    Browse Tocris compounds for FGD6

    1 HMDB Compound for FGD6    About this table
    CompoundSynonyms CAS #PubMed Ids
    Guanosine triphosphate5'-GTP (see all 10)86-01-1--
    Search CenterWatch for drugs/clinical trials and news about FGD6 

    Transcripts
    for FGD6 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    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, Sirion Biotech, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for FGD6 gene: 
    NM_018351.3  

    Unigene Cluster for FGD6:

    FYVE, RhoGEF and PH domain containing 6
    Hs.506381  [show with all ESTs]
    Unigene Representative Sequence: NM_018351
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000343958(uc001tdp.4 uc009zsx.3) ENST00000548069 ENST00000451107
    ENST00000546711(uc001tdq.1) ENST00000551521 ENST00000549499 ENST00000550368


    miRNA
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    8/85 QIAGEN miScript miRNA Assays for microRNAs that regulate FGD6 (see all 85):
    hsa-miR-193a-3p hsa-miR-128 hsa-miR-30d hsa-miR-519a hsa-miR-30a hsa-miR-3613-3p hsa-miR-155* hsa-miR-761
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    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for FGD6 (see all 7)
    OriGene shRNA RFP: FGD6
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    Clone
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    Primer
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    Additional cDNA sequence: 

    AB037783.1 AK002045.1 AK026881.1 AK124904.1 AK128492.1 BC013319.1 BC125225.1 BC125226.1 
    BX538322.1 

    6 DOTS entries:

    DT.40280918  DT.433199  DT.91811994  DT.95371363  DT.99958073  DT.95293181 

    24/89 AceView cDNA sequences (see all 89):

    CF142584 CA503082 AK128492 AI336120 AU137911 AW628588 BU183015 AA481010 
    AK124904 BP369194 BM920371 AK002045 CB140840 BG166270 BQ183345 CD644092 
    CD654093 AI275438 AA629745 BX538322 AI807284 BG251080 AA760756 AA922559 

    GeneLoc Exon Structure


    Expression
    for FGD6 gene

    (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

    FGD6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CCACTTTTAA
    FGD6 Expression
    About this image

    FGD6 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table

    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    BoneZeugopod PeriosteumBone
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Primitive gut tube-like cells (A scalable, suspensi...)

    See FGD6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for FGD6

    SOURCE GeneReport for Unigene cluster: Hs.506381
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    In Situ
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    Orthologs
    for FGD6 gene

    (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 chordates.

    Orthologs for FGD6 gene from 4/20 species (see all 20)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves FGD61 FYVE, RhoGEF and PH domain containing 6 67.62(n)
    64.84(a)    		   417908  XM_416149.3  XP_416149.3 
    lizard
    (Anolis carolinensis)    		 Reptilia FGD66
    		 --
    		 86(a)
    		 1 ↔ 1
    		 5(30926540-30964091)
    African clawed frog
    (Xenopus laevis)    		 Amphibia Xl.136592 Xenopus laevis transcribed sequence with weak similarity more 76.09(n)    BX843162.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii fgd61 FYVE, RhoGEF and PH domain containing 6 55.66(n)
    52.18(a)    		   556459  NM_001099980.1  NP_001093450.1 


    ENSEMBL Gene Tree for FGD6 (if available)
    TreeFam Gene Tree for FGD6 (if available) 

    Paralogs
    for FGD6 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for FGD6 gene
    FGD32  PLEKHF22  FGD52  PLEKHF12  FGD22  FGD42  FGD12  
    5 SIMAP similar genes for FGD6 using alignment to 6 protein entries:     FGD6_HUMAN (see all proteins):
    FGD5    FGD4    FGD2    PLEKHF2    PLEKHF1

    FGD6 for paralogs           About GeneDecksing



    Genomic Variants
    for FGD6 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/2513 NCBI SNPs in FGD6 are shown (see all 2513)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 12 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1431095491,2
    		--95470102(+) CCGCTC/TGCCTT 1 -- ds50010--------
    rs1897438781,2
    		--95470107(+) CGCCTC/TGGCCT 1 -- ds50010--------
    rs111078831,2
    		C,F--95470144(+) GAGCCA/CCCGTG 1 -- ds50013Minor allele frequency- C:0.25NA EA 124
    rs1839119211,2
    		--95470174(+) TAAATC/GTGTGA 1 -- ds50010--------
    rs1888559291,2
    		--95470176(+) AATGTA/GTGACT 1 -- ds50010--------
    rs1482733801,2
    		--95470208(+) ATCTAC/TGATGC 1 -- ds50010--------
    rs1924061461,2
    		--95470246(+) AATCCC/TAGCAC 1 -- ds50010--------
    rs1418188261,2
    		--95470265(+) GTTGAA/GGCGGG 1 -- ds50010--------
    rs1833509851,2
    		--95470367(+) TGGTGC/TGCACC 1 -- ds50010--------
    rs1173787011,2
    		F--95470507(+) GGAAAA/GAAATC 1 -- ds50011Minor allele frequency- G:0.03NA 120

    HapMap Linkage Disequilibrium report for FGD6 (95470525 - 95611258 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for FGD6
         1 CNV: 5685

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    Disorders / Diseases
    for FGD6 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    FGD6 for disorders           About MalaCards

    FGD6 for disorders           About GeneDecksing

    OMIM gene information: 613520    OMIM disorders: --

    Human Genome Epidemiology (HuGE) Navigator: FGD6 (1 document)

    Export disorders for FGD6 gene to outside databases

    Publications
    for FGD6 gene

    (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 FGD6 gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with FGD6)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10718198)1, 2 Nagase T.... Ohara O. (2000)
    4. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (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. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
    7. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)
    8. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    9. High-throughput mapping of a dynamic signaling network in mammalian cells. (PubMed id 15761153)1 Barrios-Rodiles M....Wrana J.L. (2005)
    10. Proteomic, functional, and domain-based analysis of in vivo 14-3-3 binding proteins involved in cytoskeletal regulation and cellular organization. (PubMed id 15324660)1 Jin J....Pawson T. (2004)

    External Searches for FGD6 gene

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    Genome Databases showing FGD6 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 55785 HGNC: 21740 AceView: FGD6 Ensembl:ENSG00000180263 euGenes: HUgn55785
    ECgene: FGD6 H-InvDB: FGD6

    Other Databases showing FGD6 gene

    (According to HUGE)
    About This Section
    HUGE: KIAA1362

    Specialized Databases showing FGD6 gene

    (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 FGD6 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for FGD6 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    		Patent Information for FGD6 gene:
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