Human Gene FGD3 (ENST00000375482.8_6) from GENCODE V47lift37
  Description: FYVE, RhoGEF and PH domain containing 3, transcript variant 1 (from RefSeq NM_001083536.2)
Gencode Transcript: ENST00000375482.8_6
Gencode Gene: ENSG00000127084.19_9
Transcript (Including UTRs)
   Position: hg19 chr9:95,709,805-95,798,515 Size: 88,711 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr9:95,738,539-95,797,871 Size: 59,333 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:95,709,805-95,798,515)mRNA (may differ from genome)Protein (725 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FGD3_HUMAN
DESCRIPTION: RecName: Full=FYVE, RhoGEF and PH domain-containing protein 3; AltName: Full=Zinc finger FYVE domain-containing protein 5;
FUNCTION: Promotes the formation of filopodia. May activate CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for free GTP. Plays a role in regulating the actin cytoskeleton and cell shape (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (Probable). Cytoplasm, cytoskeleton (Probable).
SIMILARITY: Contains 1 DH (DBL-homology) domain.
SIMILARITY: Contains 1 FYVE-type zinc finger.
SIMILARITY: Contains 2 PH domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: FGD3
Diseases sorted by gene-association score: aarskog-scott syndrome (10)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 83.00 RPKM in Whole Blood
Total median expression: 197.15 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -157.60424-0.372 Picture PostScript Text
3' UTR -264.40644-0.411 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000219 - DH-domain
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology
IPR000306 - Znf_FYVE
IPR017455 - Znf_FYVE-rel
IPR011011 - Znf_FYVE_PHD
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00169 - PH domain
PF00621 - RhoGEF domain
PF01363 - FYVE zinc finger

SCOP Domains:
46579 - Prefoldin
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like
57667 - beta-beta-alpha zinc fingers
57850 - RING/U-box
57889 - Cysteine-rich domain
57903 - FYVE/PHD zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2COC - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q5JSP0
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0005089 Rho guanyl-nucleotide exchange factor activity
GO:0031267 small GTPase binding
GO:0046872 metal ion binding

Biological Process:
GO:0007010 cytoskeleton organization
GO:0007186 G-protein coupled receptor signaling pathway
GO:0008360 regulation of cell shape
GO:0030036 actin cytoskeleton organization
GO:0035023 regulation of Rho protein signal transduction
GO:0043065 positive regulation of apoptotic process
GO:0043087 regulation of GTPase activity
GO:0046847 filopodium assembly
GO:0051056 regulation of small GTPase mediated signal transduction

Cellular Component:
GO:0001726 ruffle
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0030027 lamellipodium


-  Descriptions from all associated GenBank mRNAs
  BC032429 - Homo sapiens FYVE, RhoGEF and PH domain containing 3, mRNA (cDNA clone MGC:40367 IMAGE:5244790), complete cds.
AK292676 - Homo sapiens cDNA FLJ75503 complete cds.
BX647829 - Homo sapiens mRNA; cDNA DKFZp779B1817 (from clone DKFZp779B1817).
BC111054 - Homo sapiens FYVE, RhoGEF and PH domain containing 3, mRNA (cDNA clone MGC:117260 IMAGE:5751870), complete cds.
AY211386 - Homo sapiens FGD3 mRNA, complete cds.
AK225843 - Homo sapiens mRNA for FYVE, RhoGEF and PH domain containing protein 3 variant, clone: FCC126E07.
AK000004 - Homo sapiens mRNA for FLJ00004 protein, partial cds.
JD137736 - Sequence 118760 from Patent EP1572962.
JD468774 - Sequence 449798 from Patent EP1572962.
JD393175 - Sequence 374199 from Patent EP1572962.
JD443099 - Sequence 424123 from Patent EP1572962.
EU832246 - Synthetic construct Homo sapiens clone HAIB:100067275; DKFZo004F0726 FYVE, RhoGEF and PH domain containing 3 protein (FGD3) gene, encodes complete protein.
EU832153 - Synthetic construct Homo sapiens clone HAIB:100067182; DKFZo008F0725 FYVE, RhoGEF and PH domain containing 3 protein (FGD3) gene, encodes complete protein.
BC032232 - Homo sapiens FYVE, RhoGEF and PH domain containing 3, mRNA (cDNA clone IMAGE:5223488), **** WARNING: chimeric clone ****.
AK301974 - Homo sapiens cDNA FLJ58637 complete cds, highly similar to FYVE, RhoGEF and PH domain-containing protein3.
AX810690 - Sequence 14 from Patent EP1333092.
JD144373 - Sequence 125397 from Patent EP1572962.
JD415438 - Sequence 396462 from Patent EP1572962.
JD273191 - Sequence 254215 from Patent EP1572962.
JD336509 - Sequence 317533 from Patent EP1572962.
JD208571 - Sequence 189595 from Patent EP1572962.
JD071061 - Sequence 52085 from Patent EP1572962.
JD159452 - Sequence 140476 from Patent EP1572962.
JD123620 - Sequence 104644 from Patent EP1572962.
JD127656 - Sequence 108680 from Patent EP1572962.
JD267961 - Sequence 248985 from Patent EP1572962.
JD044713 - Sequence 25737 from Patent EP1572962.
JD260709 - Sequence 241733 from Patent EP1572962.
JD133035 - Sequence 114059 from Patent EP1572962.
JD495698 - Sequence 476722 from Patent EP1572962.
JD116255 - Sequence 97279 from Patent EP1572962.
JD521910 - Sequence 502934 from Patent EP1572962.
JD227116 - Sequence 208140 from Patent EP1572962.
JD477335 - Sequence 458359 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q5JSP0 (Reactome details) participates in the following event(s):

R-HSA-194913 GEFs activate Rho GTPase:GDP
R-HSA-419166 GEFs activate RhoA,B,C
R-HSA-205039 p75NTR indirectly activates RAC and Cdc42 via a guanyl-nucleotide exchange factor
R-HSA-194840 Rho GTPase cycle
R-HSA-416482 G alpha (12/13) signalling events
R-HSA-193648 NRAGE signals death through JNK
R-HSA-194315 Signaling by Rho GTPases
R-HSA-388396 GPCR downstream signalling
R-HSA-204998 Cell death signalling via NRAGE, NRIF and NADE
R-HSA-162582 Signal Transduction
R-HSA-372790 Signaling by GPCR
R-HSA-193704 p75 NTR receptor-mediated signalling
R-HSA-73887 Death Receptor Signalling

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000375482.1, ENST00000375482.2, ENST00000375482.3, ENST00000375482.4, ENST00000375482.5, ENST00000375482.6, ENST00000375482.7, F8W7P2, FGD3_HUMAN, NM_001083536, Q4VX84, Q5JSP0, Q7Z7D9, Q8N5G1, uc318mhi.1, uc318mhi.2, ZFYVE5
UCSC ID: ENST00000375482.8_6
RefSeq Accession: NM_001083536.2
Protein: Q5JSP0 (aka FGD3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.