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RAP1A RAP1A, member of RAS oncogene family [ Homo sapiens (human) ]

Gene ID: 5906, updated on 6-Nov-2022

Summary

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Official Symbol
RAP1Aprovided by HGNC
Official Full Name
RAP1A, member of RAS oncogene familyprovided by HGNC
Primary source
HGNC:HGNC:9855
See related
Ensembl:ENSG00000116473 MIM:179520; AllianceGenome:HGNC:9855
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RAP1; C21KG; G-22K; KREV1; KREV-1; SMGP21
Summary
This gene encodes a member of the Ras family of small GTPases. The encoded protein undergoes a change in conformational state and activity, depending on whether it is bound to GTP or GDP. This protein is activated by several types of guanine nucleotide exchange factors (GEFs), and inactivated by two groups of GTPase-activating proteins (GAPs). The activation status of the encoded protein is therefore affected by the balance of intracellular levels of GEFs and GAPs. The encoded protein regulates signaling pathways that affect cell proliferation and adhesion, and may play a role in tumor malignancy. Pseudogenes of this gene have been defined on chromosomes 14 and 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
Expression
Ubiquitous expression in appendix (RPKM 12.2), esophagus (RPKM 11.3) and 25 other tissues See more
Orthologs
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Genomic context

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See RAP1A in Genome Data Viewer
Location:
1p13.2
Exon count:
11
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (111542009..111716691)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (111556699..111731587)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (112084631..112259313)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 792, pseudogene Neighboring gene transmembrane and immunoglobulin domain containing 3 Neighboring gene adenosine A3 receptor Neighboring gene long intergenic non-protein coding RNA 1160 Neighboring gene uncharacterized LOC107985184 Neighboring gene Sharpr-MPRA regulatory region 155 Neighboring gene RNA, U6 small nuclear 151, pseudogene Neighboring gene keratin 18 pseudogene 57 Neighboring gene uncharacterized LOC101928718 Neighboring gene inka box actin regulator 2 Neighboring gene INKA2 antisense RNA 1 Neighboring gene DEAD-box helicase 20

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Rap1 Small GTPase Regulates Vascular Endothelial-Cadherin-Mediated Endothelial Cell-Cell Junctions and Vascular Permeability. Yamamoto K, et al. Biol Pharm Bull, 2021. PMID 34602545
  2. The Mystery of Rap1 Suppression of Oncogenic Ras. Nussinov R, et al. Trends Cancer, 2020 May. PMID 32249186, Free PMC Article
  3. Rap1 and membrane lipids cooperatively recruit talin to trigger integrin activation. Bromberger T, et al. J Cell Sci, 2019 Nov 1. PMID 31578239, Free PMC Article
  4. A Genome-wide Association Study Identifying RAP1A as a Novel Susceptibility Gene for Crohn's Disease in Japanese Individuals. Kakuta Y, et al. J Crohns Colitis, 2019 Apr 26. PMID 30500874, Free PMC Article
  5. High expression of Ras-related protein 1A promotes an aggressive phenotype in colorectal cancer via PTEN/FOXO3/CCND1 pathway. Liu L, et al. J Exp Clin Cancer Res, 2018 Jul 31. PMID 30064475, Free PMC Article

See all (270) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ArhGEF12 activates Rap1A and not RhoA in human dermal microvascular endothelial cells to reduce tumor necrosis factor-induced leak.
    Title: ArhGEF12 activates Rap1A and not RhoA in human dermal microvascular endothelial cells to reduce tumor necrosis factor-induced leak.
  2. Natural Killer Cell Transcript 4 promotes the development of Sjgren's syndrome via activation of Rap1 on B cells.
    Title: Natural Killer Cell Transcript 4 promotes the development of SjÓ§gren's syndrome via activation of Rap1 on B cells.
  3. Mechanisms of autoregulation of C3G, activator of the GTPase Rap1, and its catalytic deregulation in lymphomas.
    Title: Mechanisms of autoregulation of C3G, activator of the GTPase Rap1, and its catalytic deregulation in lymphomas.
  4. Rap1 Small GTPase Regulates Vascular Endothelial-Cadherin-Mediated Endothelial Cell-Cell Junctions and Vascular Permeability.
    Title: Rap1 Small GTPase Regulates Vascular Endothelial-Cadherin-Mediated Endothelial Cell-Cell Junctions and Vascular Permeability.
  5. Involvement of miR-337 in high glucose-suppressed osteogenic differentiation in bone marrow mesenchymal stem cells via negative regulation of Rap1A.
    Title: Involvement of miR-337 in high glucose-suppressed osteogenic differentiation in bone marrow mesenchymal stem cells via negative regulation of Rap1A.
  6. Identification of Radil as a Ras binding partner and putative activator.
    Title: Identification of Radil as a Ras binding partner and putative activator.
  7. The Mystery of Rap1 Suppression of Oncogenic Ras.
    Title: The Mystery of Rap1 Suppression of Oncogenic Ras.
  8. Large Extracellular Vesicle-Associated Rap1 Accumulates in Atherosclerotic Plaques, Correlates With Vascular Risks and Is Involved in Atherosclerosis.
    Title: Large Extracellular Vesicle-Associated Rap1 Accumulates in Atherosclerotic Plaques, Correlates With Vascular Risks and Is Involved in Atherosclerosis.
  9. Functional and structural characterization of allosteric activation of phospholipase Cepsilon by Rap1A.
    Title: Functional and structural characterization of allosteric activation of phospholipase Cε by Rap1A.
  10. Signaling diversity enabled by Rap1-regulated plasma membrane ERK with distinct temporal dynamics.
    Title: Signaling diversity enabled by Rap1-regulated plasma membrane ERK with distinct temporal dynamics.
Submit: New GeneRIF Correction See all GeneRIFs (149)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables G protein activity IEA
Inferred from Electronic Annotation
more info
  
enables GDP binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables GTP binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables guanyl-nucleotide exchange factor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-containing complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables small GTPase binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in Rap protein signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in Rap protein signal transduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cellular response to cAMP IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in cellular response to cAMP IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to nerve growth factor stimulus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in establishment of endothelial barrier IMP
Inferred from Mutant Phenotype
more info
 PubMed 
NOT involved_in microvillus assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of synaptic vesicle exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in nerve growth factor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of ERK1 and ERK2 cascade ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of GTPase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of protein kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of vasculogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein localization to plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of cell junction assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of neurotransmitter receptor localization to postsynaptic specialization membrane IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of neurotransmitter receptor localization to postsynaptic specialization membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in synaptic vesicle exocytosis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in anchoring junction IEA
Inferred from Electronic Annotation
more info
  
located_in cell junction ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in early endosome ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in endosome membrane TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of guanyl-nucleotide exchange factor complex IEA
Inferred from Electronic Annotation
more info
  
located_in late endosome ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in neuron projection IEA
Inferred from Electronic Annotation
more info
  
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in presynapse IEA
Inferred from Electronic Annotation
more info
  
located_in specific granule membrane TAS
Traceable Author Statement
more info
  
located_in sperm midpiece ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
ras-related protein Rap-1A
Names
GTP-binding protein smg p21A
Ras-related protein Krev-1
NP_001010935.1
NP_001278825.1
NP_001357145.1
NP_001357146.1
NP_001380995.1
NP_002875.1

NCBI Reference Sequences (RefSeq)

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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_001010935.3 → NP_001010935.1  ras-related protein Rap-1A precursor

    See identical proteins and their annotated locations for NP_001010935.1

    Status: REVIEWED

    Source sequence(s)
    AK094737, BC014086, BG743233, BI460853, BQ220294, BU167449, BU189979, BX473371, CA446565, DA102623, DB312010
    Consensus CDS
    CCDS840.1
    UniProtKB/Swiss-Prot
    P10113, P62834
    UniProtKB/TrEMBL
    A8KAH9
    Related
    ENSP00000509234.1, ENST00000687939.1
    Conserved Domains (1) summary
    cd04175
    Location:3 → 167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms

  2. NM_001291896.3 → NP_001278825.1  ras-related protein Rap-1A precursor

    See identical proteins and their annotated locations for NP_001278825.1

    Status: REVIEWED

    Source sequence(s)
    AL049557, AL139012
    Consensus CDS
    CCDS840.1
    UniProtKB/Swiss-Prot
    P10113, P62834
    UniProtKB/TrEMBL
    A8KAH9
    Conserved Domains (1) summary
    cd04175
    Location:3 → 167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms

  3. NM_001370216.2 → NP_001357145.1  ras-related protein Rap-1A precursor

    Status: REVIEWED

    Source sequence(s)
    AL049557, AL390195
    Consensus CDS
    CCDS840.1
    UniProtKB/Swiss-Prot
    P10113
    UniProtKB/TrEMBL
    A8KAH9
    Related
    ENSP00000348786.1, ENST00000356415.5
    Conserved Domains (1) summary
    cd04175
    Location:3 → 167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms

  4. NM_001370217.2 → NP_001357146.1  ras-related protein Rap-1A precursor

    Status: REVIEWED

    Source sequence(s)
    AL049557, AL139012
    Consensus CDS
    CCDS840.1
    UniProtKB/Swiss-Prot
    P10113
    UniProtKB/TrEMBL
    A8KAH9
    Conserved Domains (1) summary
    cd04175
    Location:3 → 167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms

  5. NM_001394066.1 → NP_001380995.1  ras-related protein Rap-1A precursor

    Status: REVIEWED

    Source sequence(s)
    AL049557, AL139012
    Consensus CDS
    CCDS840.1
    UniProtKB/Swiss-Prot
    P10113
    UniProtKB/TrEMBL
    A8KAH9
    Conserved Domains (1) summary
    cd04175
    Location:3 → 167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms

  6. NM_002884.4 → NP_002875.1  ras-related protein Rap-1A precursor

    See identical proteins and their annotated locations for NP_002875.1

    Status: REVIEWED

    Source sequence(s)
    AK094737, BC014086, BG743233, BI460853, BU167449, BU189979, BX473371, CA446565, CD108761, DA102623, DB312010
    Consensus CDS
    CCDS840.1
    UniProtKB/Swiss-Prot
    P10113, P62834
    UniProtKB/TrEMBL
    A8KAH9
    Related
    ENSP00000358723.3, ENST00000369709.4
    Conserved Domains (1) summary
    cd04175
    Location:3 → 167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    111542009..111716691
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    111556699..111731587
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P62834.1 GenPept UniProtKB/Swiss-Prot:P62834

Gene LinkOut

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