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    FGD3 FYVE, RhoGEF and PH domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 89846, updated on 8-Jul-2019

    Summary

    Official Symbol
    FGD3provided by HGNC
    Official Full Name
    FYVE, RhoGEF and PH domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:16027
    See related
    Ensembl:ENSG00000127084 MIM:617554
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ZFYVE5
    Expression
    Broad expression in spleen (RPKM 16.0), lymph node (RPKM 14.2) and 17 other tissues See more
    Orthologs

    Genomic context

    See FGD3 in Genome Data Viewer
    Location:
    9q22.31
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (92947523..93036236)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (95709601..95798518)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene sorting nexin 18 pseudogene 2 Neighboring gene arachidonate 15-lipoxygenase pseudogene 2 Neighboring gene uncharacterized LOC101927954 Neighboring gene Sharpr-MPRA regulatory region 12079 Neighboring gene sushi domain containing 3 Neighboring gene uncharacterized LOC101927993

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Pathways from BioSystems

    • Cell death signalling via NRAGE, NRIF and NADE, organism-specific biosystem (from REACTOME)
      Cell death signalling via NRAGE, NRIF and NADE, organism-specific biosystemp75NTR is a key regulator of neuronal apoptosis, both during development and after injury. Apoptosis is triggered by binding of either mature neurotrophin or proneurotrophin (proNGF, proBDNF). ProNG...
    • G alpha (12/13) signalling events, organism-specific biosystem (from REACTOME)
      G alpha (12/13) signalling events, organism-specific biosystemThe G12/13 family is probably the least well characterized subtype, partly because G12/13 coupling is difficult to determine when compared with the other subtypes which predominantly rely on assay te...
    • GPCR downstream signaling, organism-specific biosystem (from REACTOME)
      GPCR downstream signaling, organism-specific biosystemG protein-coupled receptors (GPCRs) are classically defined as the receptor, G-protein and downstream effectors, the alpha subunit of the G-protein being the primary signaling molecule. However, it h...
    • NRAGE signals death through JNK, organism-specific biosystem (from REACTOME)
      NRAGE signals death through JNK, organism-specific biosystemOnce bound by either NGF or proNGF, p75NTR interacts with NRAGE, thus leading to phosphorylation and activation of JUN Kinase (JNK). JNK controls apoptosis in two ways: it induces transcription of pr...
    • Regulation of actin cytoskeleton, organism-specific biosystem (from KEGG)
      Regulation of actin cytoskeleton, organism-specific biosystem
      Regulation of actin cytoskeleton
    • Regulation of actin cytoskeleton, conserved biosystem (from KEGG)
      Regulation of actin cytoskeleton, conserved biosystem
      Regulation of actin cytoskeleton
    • Rho GTPase cycle, organism-specific biosystem (from REACTOME)
      Rho GTPase cycle, organism-specific biosystemThe cycling of Rho GTPases is tightly controlled by three classes of protein. These are (1) guanine nucleotide dissociation inhibitors or GDIs, which maintain Rho proteins in an inactive state in the...
    • Signal Transduction, organism-specific biosystem (from REACTOME)
      Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
    • Signaling by GPCR, organism-specific biosystem (from REACTOME)
      Signaling by GPCR, organism-specific biosystemG protein-coupled receptors (GPCRs; 7TM receptors; seven transmembrane domain receptors; heptahelical receptors; G protein-linked receptors [GPLR]) are the largest family of transmembrane receptors i...
    • Signaling by Rho GTPases, organism-specific biosystem (from REACTOME)
      Signaling by Rho GTPases, organism-specific biosystemThe Rho family of small guanine nucleotide binding proteins is one of five generally recognized branches of the Ras superfamily. Like most Ras superfamily members, typical Rho proteins function as bi...
    • Signalling by NGF, organism-specific biosystem (from REACTOME)
      Signalling by NGF, organism-specific biosystemNeurotrophins (NGF, BDNF, NT-3, NT-4/5) play pivotal roles in survival, differentiation, and plasticity of neurons in the peripheral and central nervous system. They are produced, and secreted in mi...
    • p75 NTR receptor-mediated signalling, organism-specific biosystem (from REACTOME)
      p75 NTR receptor-mediated signalling, organism-specific biosystemBesides signalling through the tyrosine kinase receptors TRK A, B, and C, the mature neurotrophins NGF, BDNF, and NT3/4 signal through their common receptor p75NTR. NGF binding to p75NTR activates a ...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ00004, MGC117260

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    Rho guanyl-nucleotide exchange factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    guanyl-nucleotide exchange factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    small GTPase binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    G protein-coupled receptor signaling pathway TAS
    Traceable Author Statement
    more info
     
    actin cytoskeleton organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cytoskeleton organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    filopodium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of apoptotic process TAS
    Traceable Author Statement
    more info
     
    regulation of GTPase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of Rho protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of cell shape ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of small GTPase mediated signal transduction TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    lamellipodium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    ruffle ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    FYVE, RhoGEF and PH domain-containing protein 3
    Names
    FGD1 family, member 3
    faciogenital dysplasia 3
    zinc finger FYVE domain-containing protein 5

    NCBI Reference Sequences (RefSeq)

    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)

    1. NM_001083536.2NP_001077005.1  FYVE, RhoGEF and PH domain-containing protein 3 isoform a

      See identical proteins and their annotated locations for NP_001077005.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1, 2, and 4 all encode the same isoform (a).
      Source sequence(s)
      AL451065, BC032429, BF509875, DA493667
      Consensus CDS
      CCDS43849.1
      UniProtKB/Swiss-Prot
      Q5JSP0
      UniProtKB/TrEMBL
      A0A024R252
      Related
      ENSP00000364631.3, ENST00000375482.8
      Conserved Domains (4) summary
      cd00160
      Location:160339
      RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
      cd13236
      Location:598702
      PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
      cd13387
      Location:371478
      PH1_FGD3; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 3, N-terminal Pleckstrin homology (PH) domain
      cd15740
      Location:531584
      FYVE_FGD3; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 3 (FGD3) and similar proteins
    2. NM_001286993.1NP_001273922.1  FYVE, RhoGEF and PH domain-containing protein 3 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is 1 aa shorter than isoform a.
      Source sequence(s)
      AK225843, AK292676, AY211386, BF510761
      Consensus CDS
      CCDS69619.1
      UniProtKB/Swiss-Prot
      Q5JSP0
      UniProtKB/TrEMBL
      A8K9G1
      Related
      ENSP00000413833.2, ENST00000416701.6
      Conserved Domains (5) summary
      cd13236
      Location:597701
      PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
      cd13387
      Location:371478
      PH1_FGD3; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 3, N-terminal Pleckstrin homology (PH) domain
      cd15740
      Location:531584
      FYVE_FGD3; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 3 (FGD3) and similar proteins
      pfam00169
      Location:371469
      PH; PH domain
      pfam00621
      Location:161340
      RhoGEF; RhoGEF domain
    3. NM_001369951.1NP_001356880.1  FYVE, RhoGEF and PH domain-containing protein 3 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4), as well as variants 1 and 2, encodes the longest isoform (a).
      Source sequence(s)
      AL389924, AL451065
      Related
      ENSP00000496819.1, ENST00000468206.6
      Conserved Domains (4) summary
      cd00160
      Location:160339
      RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
      cd13236
      Location:598702
      PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
      cd13387
      Location:371478
      PH1_FGD3; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 3, N-terminal Pleckstrin homology (PH) domain
      cd15740
      Location:531584
      FYVE_FGD3; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 3 (FGD3) and similar proteins
    4. NM_001369952.1NP_001356881.1  FYVE, RhoGEF and PH domain-containing protein 3 isoform c

      Status: VALIDATED

      Source sequence(s)
      AL389924, AL451065
      Conserved Domains (4) summary
      cd00160
      Location:160339
      RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
      cd13236
      Location:549653
      PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
      cd15740
      Location:482535
      FYVE_FGD3; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 3 (FGD3) and similar proteins
      cl17171
      Location:345429
      PH-like; Pleckstrin homology-like domain
    5. NM_033086.2NP_149077.2  FYVE, RhoGEF and PH domain-containing protein 3 isoform a

      See identical proteins and their annotated locations for NP_149077.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 4 all encode the same isoform (a).
      Source sequence(s)
      AL451065, BC111054, BF509875, DB161711
      Consensus CDS
      CCDS43849.1
      UniProtKB/Swiss-Prot
      Q5JSP0
      UniProtKB/TrEMBL
      A0A024R252
      Related
      ENSP00000336914.6, ENST00000337352.10
      Conserved Domains (4) summary
      cd00160
      Location:160339
      RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
      cd13236
      Location:598702
      PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
      cd13387
      Location:371478
      PH1_FGD3; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 3, N-terminal Pleckstrin homology (PH) domain
      cd15740
      Location:531584
      FYVE_FGD3; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 3 (FGD3) and similar proteins

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

      Range
      92947523..93036236
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017015274.1XP_016870763.1  FYVE, RhoGEF and PH domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      Q5JSP0
      UniProtKB/TrEMBL
      A0A024R252
      Conserved Domains (4) summary
      cd00160
      Location:160339
      RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
      cd13236
      Location:598702
      PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
      cd13387
      Location:371478
      PH1_FGD3; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 3, N-terminal Pleckstrin homology (PH) domain
      cd15740
      Location:531584
      FYVE_FGD3; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 3 (FGD3) and similar proteins

    RNA

    1. XR_001746414.2 RNA Sequence

    2. XR_002956823.1 RNA Sequence

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