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Aliases for RAPGEF3 Gene

Aliases for RAPGEF3 Gene

  • Rap Guanine Nucleotide Exchange Factor 3 2 3 5
  • Exchange Protein Directly Activated By CAMP 1 2 3 4
  • Rap1 Guanine-Nucleotide-Exchange Factor Directly Activated By CAMP 3 4
  • CAMP-Regulated Guanine Nucleotide Exchange Factor I 3 4
  • Rap Guanine Nucleotide Exchange Factor (GEF) 3 2 3
  • Exchange Factor Directly Activated By CAMP 1 3 4
  • CAMP-GEFI 3 4
  • EPAC 1 3 4
  • EPAC1 3 4
  • EPAC 3 4
  • RAP Guanine-Nucleotide-Exchange Factor (GEF) 3 2
  • 9330170P05Rik 3
  • HSU79275 3
  • Bcm910 3
  • CGEF1 4

External Ids for RAPGEF3 Gene

Previous GeneCards Identifiers for RAPGEF3 Gene

  • GC12M046418
  • GC12M046419
  • GC12M048128
  • GC12M045159

Summaries for RAPGEF3 Gene

GeneCards Summary for RAPGEF3 Gene

RAPGEF3 (Rap Guanine Nucleotide Exchange Factor 3) is a Protein Coding gene. Diseases associated with RAPGEF3 include Leukocyte Adhesion Deficiency, Type Iii and Asthma. Among its related pathways are Integrin alphaIIb beta3 signaling and Platelet activation, signaling and aggregation. GO annotations related to this gene include guanyl-nucleotide exchange factor activity and cAMP-dependent protein kinase regulator activity. An important paralog of this gene is RAPGEF4.

UniProtKB/Swiss-Prot for RAPGEF3 Gene

  • Guanine nucleotide exchange factor (GEF) for RAP1A and RAP2A small GTPases that is activated by binding cAMP. Through simultaneous binding of PDE3B to RAPGEF3 and PIK3R6 is assembled in a signaling complex in which it activates the PI3K gamma complex and which is involved in angiogenesis. Plays a role in the modulation of the cAMP-induced dynamic control of endothelial barrier function through a pathway that is independent on Rho-mediated signaling. Required for the actin rearrangement at cell-cell junctions, such as stress fibers and junctional actin.

Tocris Summary for RAPGEF3 Gene

  • GTPases are a group of enzymes that catalyze hydrolysis of the gamma phosphate bond in guanine triphosphate (GTP) to form guanine diphosphate (GDP). Mg2+ ions are essential for catalytic activity. GTPases, often coupled to G proteins, are essential in signal transduction.

Gene Wiki entry for RAPGEF3 Gene

No data available for Entrez Gene Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RAPGEF3 Gene

Genomics for RAPGEF3 Gene

Regulatory Elements for RAPGEF3 Gene

Enhancers for RAPGEF3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
- Elite enhancer/Elite enhancer-gene association

Enhancers around RAPGEF3 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the RAPGEF3 gene promoter:

Genomic Location for RAPGEF3 Gene

Chromosome:
12
Start:
47,734,367 bp from pter
End:
47,771,040 bp from pter
Size:
36,674 bases
Orientation:
Minus strand

Genomic View for RAPGEF3 Gene

Genes around RAPGEF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAPGEF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAPGEF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAPGEF3 Gene

Proteins for RAPGEF3 Gene

  • Protein details for RAPGEF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95398-RPGF3_HUMAN
    Recommended name:
    Rap guanine nucleotide exchange factor 3
    Protein Accession:
    O95398
    Secondary Accessions:
    • A8K2G5
    • E7EQC8
    • O95634
    • Q8WVN0

    Protein attributes for RAPGEF3 Gene

    Size:
    923 amino acids
    Molecular mass:
    103751 Da
    Quaternary structure:
    • Interacts with PDE3B.
    SequenceCaution:
    • Sequence=AAD02890.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAD12740.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for RAPGEF3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RAPGEF3 Gene

Post-translational modifications for RAPGEF3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for RAPGEF3 (Epac1)

No data available for DME Specific Peptides for RAPGEF3 Gene

Domains & Families for RAPGEF3 Gene

Gene Families for RAPGEF3 Gene

IUPHAR :

Graphical View of Domain Structure for InterPro Entry

O95398

UniProtKB/Swiss-Prot:

RPGF3_HUMAN :
  • The DEP domain is involved in membrane localization independent from regulation by cAMP.
Domain:
  • The DEP domain is involved in membrane localization independent from regulation by cAMP.
  • Contains 1 cyclic nucleotide-binding domain.
  • Contains 1 DEP domain.
  • Contains 1 N-terminal Ras-GEF domain.
  • Contains 1 Ras-GEF domain.
genes like me logo Genes that share domains with RAPGEF3: view

Function for RAPGEF3 Gene

Molecular function for RAPGEF3 Gene

UniProtKB/Swiss-Prot Function:
Guanine nucleotide exchange factor (GEF) for RAP1A and RAP2A small GTPases that is activated by binding cAMP. Through simultaneous binding of PDE3B to RAPGEF3 and PIK3R6 is assembled in a signaling complex in which it activates the PI3K gamma complex and which is involved in angiogenesis. Plays a role in the modulation of the cAMP-induced dynamic control of endothelial barrier function through a pathway that is independent on Rho-mediated signaling. Required for the actin rearrangement at cell-cell junctions, such as stress fibers and junctional actin.

Gene Ontology (GO) - Molecular Function for RAPGEF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity EXP 15334074
GO:0005515 protein binding IPI 21393242
GO:0017034 Rap guanyl-nucleotide exchange factor activity IMP 21840392
GO:0019904 protein domain specific binding IPI 21047789
GO:0030552 cAMP binding IEA --
genes like me logo Genes that share ontologies with RAPGEF3: view
genes like me logo Genes that share phenotypes with RAPGEF3: view

Animal Models for RAPGEF3 Gene

MGI Knock Outs for RAPGEF3:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RAPGEF3 Gene

Localization for RAPGEF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAPGEF3 Gene

Endomembrane system.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RAPGEF3 Gene COMPARTMENTS Subcellular localization image for RAPGEF3 gene
Compartment Confidence
extracellular 5
plasma membrane 5
cytosol 4
nucleus 3
cytoskeleton 2
endoplasmic reticulum 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for RAPGEF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005902 microvillus IDA 21047789
GO:0009925 basal plasma membrane IEA --
GO:0012505 endomembrane system IEA --
GO:0016020 membrane TAS 10777494
genes like me logo Genes that share ontologies with RAPGEF3: view

Pathways & Interactions for RAPGEF3 Gene

genes like me logo Genes that share pathways with RAPGEF3: view

Gene Ontology (GO) - Biological Process for RAPGEF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis IEA --
GO:0007165 signal transduction TAS 9853756
GO:0007420 brain development IEA --
GO:0008283 cell proliferation TAS 9853756
GO:0010667 negative regulation of cardiac muscle cell apoptotic process IEA --
genes like me logo Genes that share ontologies with RAPGEF3: view

No data available for SIGNOR curated interactions for RAPGEF3 Gene

Drugs & Compounds for RAPGEF3 Gene

(18) Drugs for RAPGEF3 Gene - From: ApexBio, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
cyclic amp Experimental Pharma 0
Guanosine diphosphate Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
8-CPT-2Me-cAMP, sodium salt Pharma EPAC agonist, selective, Selective Epac activator 0

(7) Additional Compounds for RAPGEF3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(5) Tocris Compounds for RAPGEF3 Gene

Compound Action Cas Number
8-CPT-2Me-cAMP, sodium salt Selective Epac activator 634207-53-7
8-pCPT-2-O-Me-cAMP-AM Selective Epac activator; cell-permeable analog of 8CPT-2Me-cAMP (Cat. No. 1645) 1152197-23-3
Dynasore Non-competitive dynamin inhibitor 304448-55-3
Mdivi 1 Dynamin inhibitor; attenuates mitochondrial division and apoptosis 338967-87-6
ML 141 Selective inhibitor of Cdc42 Rho family GTPase 71203-35-5

(4) ApexBio Compounds for RAPGEF3 Gene

Compound Action Cas Number
8-CPT-2Me-cAMP, sodium salt EPAC agonist, selective 634207-53-7
8-pCPT-2-O-Me-cAMP-AM 1152197-23-3
MitMAB 1119-97-7
OctMAB 1120-02-1
genes like me logo Genes that share compounds with RAPGEF3: view

Drug Products

Transcripts for RAPGEF3 Gene

Unigene Clusters for RAPGEF3 Gene

Rap guanine nucleotide exchange factor (GEF) 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for RAPGEF3 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^
SP1: - - - -
SP2: - - -
SP3: - - - - - - - -
SP4:
SP5:
SP6: - -
SP7: -
SP8:
SP9:
SP10:
SP11:

ExUns: 20a · 20b · 20c ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28a · 28b ^ 29a · 29b · 29c · 29d
SP1: - -
SP2: - - -
SP3: - -
SP4: - -
SP5:
SP6:
SP7:
SP8:
SP9: - -
SP10:
SP11: -

Relevant External Links for RAPGEF3 Gene

GeneLoc Exon Structure for
RAPGEF3
ECgene alternative splicing isoforms for
RAPGEF3

Expression for RAPGEF3 Gene

mRNA expression in normal human tissues for RAPGEF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RAPGEF3 Gene

This gene is overexpressed in Urine (34.6) and Fetal Brain (34.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RAPGEF3 Gene



Protein tissue co-expression partners for RAPGEF3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RAPGEF3 Gene:

RAPGEF3

SOURCE GeneReport for Unigene cluster for RAPGEF3 Gene:

Hs.8578

mRNA Expression by UniProt/SwissProt for RAPGEF3 Gene:

O95398-RPGF3_HUMAN
Tissue specificity: Widely expressed with highest levels in adult kidney, heart, thyroid and brain, and fetal kidney.
genes like me logo Genes that share expression patterns with RAPGEF3: view

Primer Products

No data available for mRNA differential expression in normal tissues for RAPGEF3 Gene

Orthologs for RAPGEF3 Gene

This gene was present in the common ancestor of animals.

Orthologs for RAPGEF3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia RAPGEF3 34
  • 90.86 (n)
  • 93.72 (a)
RAPGEF3 35
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RAPGEF3 34
  • 91.83 (n)
  • 94.55 (a)
RAPGEF3 35
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rapgef3 34
  • 87.97 (n)
  • 91.01 (a)
Rapgef3 16
Rapgef3 35
  • 90 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RAPGEF3 34
  • 99.75 (n)
  • 99.78 (a)
RAPGEF3 35
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rapgef3 34
  • 87.48 (n)
  • 91.15 (a)
chicken
(Gallus gallus)
Aves RAPGEF3 34
  • 70.73 (n)
  • 69.2 (a)
RAPGEF3 35
  • 66 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RAPGEF3 35
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rapgef3 34
  • 63.69 (n)
  • 60.76 (a)
zebrafish
(Danio rerio)
Actinopterygii LOC101886094 34
  • 60.82 (n)
  • 57.41 (a)
rapgef3 35
  • 54 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Epac 35
  • 35 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea epac-1 35
  • 28 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 38 (a)
OneToMany
Species where no ortholog for RAPGEF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RAPGEF3 Gene

ENSEMBL:
Gene Tree for RAPGEF3 (if available)
TreeFam:
Gene Tree for RAPGEF3 (if available)

Paralogs for RAPGEF3 Gene

genes like me logo Genes that share paralogs with RAPGEF3: view

Variants for RAPGEF3 Gene

Sequence variations from dbSNP and Humsavar for RAPGEF3 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
VAR_047924 -
rs2016123 - 47,751,142(+) AGTTC(C/T)CACGG nc-transcript-variant, reference, missense
rs12422983 - 47,748,853(+) AGGGC(C/T)GGCGC nc-transcript-variant, upstream-variant-2KB, reference, missense
rs61709815 - 47,747,550(+) TGTGG(C/T)ATCGC nc-transcript-variant, reference, missense, utr-variant-3-prime
rs7308032 -- 47,744,239(+) TGGGA(A/C)CAAGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RAPGEF3 Gene

Variant ID Type Subtype PubMed ID
dgv94n21 CNV loss 19592680
nsv470289 CNV gain 18288195
nsv518315 CNV loss 19592680
nsv696 CNV insertion 18451855

Variation tolerance for RAPGEF3 Gene

Residual Variation Intolerance Score: 74.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.77; 93.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RAPGEF3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAPGEF3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAPGEF3 Gene

Disorders for RAPGEF3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for RAPGEF3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
leukocyte adhesion deficiency, type iii
  • leukocyte adhesion deficiency, type 3
asthma
  • asthma, protection against
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for RAPGEF3

Genetic Association Database (GAD)
RAPGEF3
Human Genome Epidemiology (HuGE) Navigator
RAPGEF3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RAPGEF3
genes like me logo Genes that share disorders with RAPGEF3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RAPGEF3 Gene

Publications for RAPGEF3 Gene

  1. Association study of the Epac gene and tobacco smoking and nicotine dependence. (PMID: 15274052) Chen X. … Kendler K.S. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2004) 3 22 46 65
  2. Mechanism of regulation of the Epac family of cAMP-dependent RapGEFs. (PMID: 10777494) de Rooij J. … Bos J.L. (J. Biol. Chem. 2000) 2 3 4 65
  3. A family of cAMP-binding proteins that directly activate rap1. (PMID: 9856955) Kawasaki H. … Graybiel A.M. (Science 1998) 2 3 4 65
  4. Epac is a Rap1 guanine-nucleotide-exchange factor directly activated by cyclic AMP. (PMID: 9853756) de Rooij J. … Bos J.L. (Nature 1998) 3 4 22 65
  5. A phosphodiesterase 3B-based signaling complex integrates exchange protein activated by cAMP 1 and phosphatidylinositol 3-kinase signals in human arterial endothelial cells. (PMID: 21393242) Wilson L.S. … Maurice D.H. (J. Biol. Chem. 2011) 3 4 65

Products for RAPGEF3 Gene

Sources for RAPGEF3 Gene

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