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RAPGEF3 Rap guanine nucleotide exchange factor 3 [ Homo sapiens (human) ]

Gene ID: 10411, updated on 7-Jun-2020

Summary

Official Symbol
RAPGEF3provided by HGNC
Official Full Name
Rap guanine nucleotide exchange factor 3provided by HGNC
Primary source
HGNC:HGNC:16629
See related
Ensembl:ENSG00000079337 MIM:606057
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
EPAC; EPAC1; bcm910; HSU79275; CAMP-GEFI
Expression
Broad expression in fat (RPKM 15.0), thyroid (RPKM 13.2) and 22 other tissues See more
Orthologs

Genomic context

See RAPGEF3 in Genome Data Viewer
Location:
12q13.11
Exon count:
29
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (47734363..47758880, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (48128453..48164846, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene RNA polymerase II associated protein 3 Neighboring gene Sharpr-MPRA regulatory region 11797 Neighboring gene uncharacterized LOC105369748 Neighboring gene endonuclease, poly(U) specific Neighboring gene solute carrier family 48 member 1 Neighboring gene histone deacetylase 7 Neighboring gene long intergenic non-protein coding RNA 2354

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of Rap guanine nucleotide exchange factor (GEF) 3 (RAPGEF3; CAMP-GEFI) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N PubMed
Knockdown of Rap guanine nucleotide exchange factor 3 (RAPGEF3; CAMP-GEFI) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Protein interactions

Protein Gene Interaction Pubs
capsid gag Prostaglandin E2-mediated HIV-1 inhibition requires the EPAC/RAP/RhoA signaling pathway by downregulation of HIV-1 CA production PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC21410

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rap guanyl-nucleotide exchange factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
cAMP binding IEA
Inferred from Electronic Annotation
more info
 
guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Rap protein signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
angiogenesis IEA
Inferred from Electronic Annotation
more info
 
cAMP-mediated signaling NAS
Non-traceable Author Statement
more info
PubMed 
cellular response to cAMP IDA
Inferred from Direct Assay
more info
PubMed 
establishment of endothelial barrier IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of syncytium formation by plasma membrane fusion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of GTPase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of angiogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of peptidyl-serine phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of protein acetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein export from nucleus IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of stress fiber assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of syncytium formation by plasma membrane fusion IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of actin cytoskeleton reorganization IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT regulation of histone H3-K9 acetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of insulin secretion TAS
Traceable Author Statement
more info
 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
colocalizes_with cortical actin cytoskeleton IDA
Inferred from Direct Assay
more info
PubMed 
endomembrane system IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
filopodium IDA
Inferred from Direct Assay
more info
PubMed 
lamellipodium IDA
Inferred from Direct Assay
more info
PubMed 
membrane TAS
Traceable Author Statement
more info
PubMed 
microvillus IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
rap guanine nucleotide exchange factor 3
Names
9330170P05Rik
EPAC 1
Rap guanine nucleotide exchange factor (GEF) 3
Rap1 guanine-nucleotide-exchange factor directly activated by cAMP
cAMP-regulated guanine nucleotide exchange factor I
exchange factor directly activated by cAMP 1
exchange protein directly activated by cAMP 1

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_001098531.4NP_001092001.2  rap guanine nucleotide exchange factor 3 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC004241
    Consensus CDS
    CCDS41775.1
    Related
    ENSP00000395708.2, ENST00000449771.7
  2. NM_001098532.2NP_001092002.1  rap guanine nucleotide exchange factor 3 isoform b

    See identical proteins and their annotated locations for NP_001092002.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' end and differs in the 5' UTR, compared to variant 1. These differences cause translation initiation at a downstream AUG and an isoform (b) with a shorter N-terminus compared to isoform a. Variants 2 and 3 encode the same isoform.
    Source sequence(s)
    AC004241, AK092448, BQ007070, CN294139, DB179165, DB278856, U79275
    Consensus CDS
    CCDS31784.1
    UniProtKB/Swiss-Prot
    O95398
    UniProtKB/TrEMBL
    Q99777
    Conserved Domains (5) summary
    cd06224
    Location:350469
    REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
    COG0664
    Location:226304
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:205314
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cd00155
    Location:616848
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
    cd04437
    Location:58181
    DEP_Epac; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in Epac-like proteins. Epac (exchange proteins directly activated by cAMP) proteins are GEFs (guanine-nucleotide-exchange factors) for the small GTPases, Rap1 and Rap2. They are directly regulated by ...
  3. NM_006105.5NP_006096.2  rap guanine nucleotide exchange factor 3 isoform b

    See identical proteins and their annotated locations for NP_006096.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' exon and differs in the 5' UTR, compared to variant 1. These differences cause translation initiation at a downstream AUG and an isoform (b) with a shorter N-terminus compared to isoform a. Variants 2 and 3 encode the same isoform.
    Source sequence(s)
    AC004241, AK092448, BQ007070, CN294139, DA629958, U79275
    Consensus CDS
    CCDS31784.1
    UniProtKB/Swiss-Prot
    O95398
    UniProtKB/TrEMBL
    Q99777
    Related
    ENSP00000384521.2, ENST00000405493.6
    Conserved Domains (5) summary
    cd06224
    Location:350469
    REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
    COG0664
    Location:226304
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:205314
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cd00155
    Location:616848
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
    cd04437
    Location:58181
    DEP_Epac; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in Epac-like proteins. Epac (exchange proteins directly activated by cAMP) proteins are GEFs (guanine-nucleotide-exchange factors) for the small GTPases, Rap1 and Rap2. They are directly regulated by ...

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_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    47734363..47758880 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011537752.2XP_011536054.1  rap guanine nucleotide exchange factor 3 isoform X1

    Conserved Domains (5) summary
    cd06224
    Location:407526
    REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
    COG0664
    Location:283361
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:262371
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cd00155
    Location:673905
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
    cd04437
    Location:100238
    DEP_Epac; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in Epac-like proteins. Epac (exchange proteins directly activated by cAMP) proteins are GEFs (guanine-nucleotide-exchange factors) for the small GTPases, Rap1 and Rap2. They are directly regulated by ...
  2. XM_011537758.2XP_011536060.1  rap guanine nucleotide exchange factor 3 isoform X3

    Related
    ENST00000482843.5
    Conserved Domains (5) summary
    cd06224
    Location:248367
    REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
    COG0664
    Location:124202
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:103212
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cd00155
    Location:514746
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
    cl02442
    Location:3279
    DEP; DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is ...
  3. XM_011537755.1XP_011536057.1  rap guanine nucleotide exchange factor 3 isoform X2

    Related
    ENSP00000448480.1, ENST00000548919.5
    Conserved Domains (5) summary
    cd06224
    Location:365484
    REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
    COG0664
    Location:241319
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:220329
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cd00155
    Location:631863
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
    cd04437
    Location:58196
    DEP_Epac; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in Epac-like proteins. Epac (exchange proteins directly activated by cAMP) proteins are GEFs (guanine-nucleotide-exchange factors) for the small GTPases, Rap1 and Rap2. They are directly regulated by ...
  4. XM_005268571.3XP_005268628.1  rap guanine nucleotide exchange factor 3 isoform X5

    Conserved Domains (2) summary
    cd06224
    Location:183
    REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
    cd00155
    Location:230462
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
  5. XM_024448795.1XP_024304563.1  rap guanine nucleotide exchange factor 3 isoform X5

    Related
    ENST00000479866.5
    Conserved Domains (2) summary
    cd06224
    Location:183
    REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
    cd00155
    Location:230462
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
  6. XM_017018688.2XP_016874177.1  rap guanine nucleotide exchange factor 3 isoform X4

    Related
    ENSP00000378764.3, ENST00000395358.7

RNA

  1. XR_001748550.2 RNA Sequence

  2. XR_002957282.1 RNA Sequence

  3. XR_001748551.2 RNA Sequence

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