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

Gene ID: 89846, updated on 1-Jun-2020

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
109.20200522 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

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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
 
filopodium assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 Updated Annotation Release 109.

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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