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RAPGEF4 Rap guanine nucleotide exchange factor 4 [ Homo sapiens (human) ]

Gene ID: 11069, updated on 1-Aug-2020

Summary

Official Symbol
RAPGEF4provided by HGNC
Official Full Name
Rap guanine nucleotide exchange factor 4provided by HGNC
Primary source
HGNC:HGNC:16626
See related
Ensembl:ENSG00000091428 MIM:606058
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; CGEF2; EPAC2; EPAC 2; Nbla00496; CAMP-GEFII
Expression
Biased expression in brain (RPKM 37.0), adrenal (RPKM 17.3) and 12 other tissues See more
Orthologs

Genomic context

See RAPGEF4 in Genome Data Viewer
Location:
2q31.1
Exon count:
37
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (172735282..173052893)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (173600525..173917621)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 4236 Neighboring gene pyruvate dehydrogenase kinase 1 Neighboring gene RAPGEF4 antisense RNA 1 Neighboring gene aldehyde dehydrogenase 7 family member A1 pseudogene 2 Neighboring gene mitogen-activated protein kinase kinase kinase 20 Neighboring gene MAP3K20 antisense RNA 1 Neighboring gene VISTA enhancer hs242 Neighboring gene uncharacterized LOC105373743

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?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
NHGRI GWA Catalog

HIV-1 interactions

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Ras GTPase binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Ras guanyl-nucleotide exchange factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
cAMP binding ISS
Inferred from Sequence or Structural Similarity
more info
 
guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
G protein-coupled receptor signaling pathway TAS
Traceable Author Statement
more info
PubMed 
cAMP-mediated signaling IEA
Inferred from Electronic Annotation
more info
 
calcium ion regulated exocytosis IEA
Inferred from Electronic Annotation
more info
 
insulin secretion IEA
Inferred from Electronic Annotation
more info
 
regulation of exocytosis IEA
Inferred from Electronic Annotation
more info
 
regulation of insulin secretion TAS
Traceable Author Statement
more info
 
regulation of synaptic vesicle cycle IEA
Inferred from Electronic Annotation
more info
 
small GTPase mediated signal transduction IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IEA
Inferred from Electronic Annotation
more info
 
hippocampal mossy fiber to CA3 synapse IEA
Inferred from Electronic Annotation
more info
 
membrane TAS
Traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
rap guanine nucleotide exchange factor 4
Names
RAP guanine-nucleotide-exchange factor (GEF) 4
Rap guanine nucleotide exchange factor (GEF) 4
cAMP-regulated guanine nucleotide exchange factor II
exchange factor directly activated by cAMP 2
exchange protein directly activated by cAMP 2
putative protein product of Nbla00496

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_001100397.2NP_001093867.1  rap guanine nucleotide exchange factor 4 isoform b

    See identical proteins and their annotated locations for NP_001093867.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in its 5' UTR, lacks several exons in the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AC009484, AC019046, AC104086
    Consensus CDS
    CCDS42776.1
    UniProtKB/Swiss-Prot
    Q8WZA2
    Related
    ENSP00000380276.3, ENST00000397087.7
    Conserved Domains (4) summary
    smart00147
    Location:624865
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    cd00038
    Location:212323
    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 ...
    cd04437
    Location:62190
    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 ...
    pfam00618
    Location:355461
    RasGEF_N; RasGEF N-terminal motif
  2. NM_001282899.2NP_001269828.1  rap guanine nucleotide exchange factor 4 isoform c

    See identical proteins and their annotated locations for NP_001269828.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in its 5' UTR, lacks several exons in the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AC009484, AC019046, AC104086
    Consensus CDS
    CCDS63060.1
    UniProtKB/Swiss-Prot
    Q8WZA2
    Related
    ENSP00000440250.1, ENST00000540783.5
    Conserved Domains (4) summary
    smart00147
    Location:615856
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    cd00038
    Location:203314
    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 ...
    cd04437
    Location:53181
    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 ...
    pfam00618
    Location:346452
    RasGEF_N; RasGEF N-terminal motif
  3. NM_001282900.2NP_001269829.1  rap guanine nucleotide exchange factor 4 isoform d

    See identical proteins and their annotated locations for NP_001269829.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in its 5' UTR, lacks several exons in the 5' coding region, initiates translation at a downstream in-frame start codon, and lacks an additional in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AC009484, AC019046, AC104086
    Consensus CDS
    CCDS63061.1
    UniProtKB/Swiss-Prot
    Q8WZA2
    Related
    ENSP00000440135.1, ENST00000538974.5
    Conserved Domains (4) summary
    smart00147
    Location:597838
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    cd00038
    Location:185296
    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 ...
    cd04437
    Location:35163
    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 ...
    pfam00618
    Location:328434
    RasGEF_N; RasGEF N-terminal motif
  4. NM_001282901.2NP_001269830.1  rap guanine nucleotide exchange factor 4 isoform e

    See identical proteins and their annotated locations for NP_001269830.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in its 5' UTR, lacks several exons in the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (e) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AC009484, AC019046, AC104086
    Consensus CDS
    CCDS74604.1
    UniProtKB/Swiss-Prot
    Q8WZA2
    UniProtKB/TrEMBL
    B7Z278
    Related
    ENSP00000438011.1, ENST00000535187.5
    Conserved Domains (4) summary
    smart00147
    Location:548789
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    cd00038
    Location:136247
    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 ...
    cd04437
    Location:1114
    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 ...
    pfam00618
    Location:279385
    RasGEF_N; RasGEF N-terminal motif
  5. NM_001375864.1NP_001362793.1  rap guanine nucleotide exchange factor 4 isoform f

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
  6. NM_001375865.1NP_001362794.1  rap guanine nucleotide exchange factor 4 isoform g

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
  7. NM_001375866.1NP_001362795.1  rap guanine nucleotide exchange factor 4 isoform h

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
  8. NM_001375867.1NP_001362796.1  rap guanine nucleotide exchange factor 4 isoform i

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
  9. NM_001375868.1NP_001362797.1  rap guanine nucleotide exchange factor 4 isoform j

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
  10. NM_001375869.1NP_001362798.1  rap guanine nucleotide exchange factor 4 isoform k

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
  11. NM_001375870.1NP_001362799.1  rap guanine nucleotide exchange factor 4 isoform l

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
  12. NM_001375871.1NP_001362800.1  rap guanine nucleotide exchange factor 4 isoform m

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
  13. NM_001375872.1NP_001362801.1  rap guanine nucleotide exchange factor 4 isoform n

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
    Related
    ENSP00000387104.1, ENST00000409036.5
  14. NM_001375873.1NP_001362802.1  rap guanine nucleotide exchange factor 4 isoform o

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
  15. NM_001375874.1NP_001362803.1  rap guanine nucleotide exchange factor 4 isoform p

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
  16. NM_001375875.1NP_001362804.1  rap guanine nucleotide exchange factor 4 isoform q

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC104086
  17. NM_001375876.1NP_001362805.1  rap guanine nucleotide exchange factor 4 isoform r

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC104086
  18. NM_007023.4NP_008954.2  rap guanine nucleotide exchange factor 4 isoform a

    See identical proteins and their annotated locations for NP_008954.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
    Consensus CDS
    CCDS42775.1
    UniProtKB/Swiss-Prot
    Q8WZA2
    Related
    ENSP00000380271.3, ENST00000397081.8
    Conserved Domains (4) summary
    smart00147
    Location:7681009
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    cd00038
    Location:43158
    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 ...
    cd04437
    Location:206334
    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 ...
    pfam00618
    Location:499605
    RasGEF_N; RasGEF N-terminal motif

RNA

  1. NR_164739.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
  2. NR_164740.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086
  3. NR_164741.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC009484, AC018712, AC019046, AC104086

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    172735282..173052893
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006712205.3XP_006712268.1  rap guanine nucleotide exchange factor 4 isoform X5

    See identical proteins and their annotated locations for XP_006712268.1

    UniProtKB/Swiss-Prot
    Q8WZA2
    Conserved Domains (4) summary
    smart00147
    Location:597838
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    cd00038
    Location:185296
    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 ...
    cd04437
    Location:35163
    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 ...
    pfam00618
    Location:328434
    RasGEF_N; RasGEF N-terminal motif
  2. XM_011510505.3XP_011508807.1  rap guanine nucleotide exchange factor 4 isoform X3

    Conserved Domains (5) summary
    smart00147
    Location:638879
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    COG0664
    Location:221328
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:226337
    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 ...
    cd04437
    Location:76204
    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 ...
    pfam00618
    Location:369475
    RasGEF_N; RasGEF N-terminal motif
  3. XM_017003196.2XP_016858685.1  rap guanine nucleotide exchange factor 4 isoform X2

  4. XM_017003197.1XP_016858686.1  rap guanine nucleotide exchange factor 4 isoform X4

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