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

Gene ID: 5906, updated on 13-Jan-2020

Summary

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
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

Genomic context

See RAP1A in Genome Data Viewer
Location:
1p13.2
Exon count:
12
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (111542009..111716695)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (112162405..112256807)

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

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
An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits.
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
GDP binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
GTP binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Rap guanyl-nucleotide exchange factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
Rap protein signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Rap protein signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to cAMP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to cAMP IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to drug IEA
Inferred from Electronic Annotation
more info
 
cellular response to glucose stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to nerve growth factor stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
establishment of endothelial barrier IMP
Inferred from Mutant Phenotype
more info
PubMed 
liver regeneration IEA
Inferred from Electronic Annotation
more info
 
NOT microvillus assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of collagen biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of synaptic vesicle exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nerve growth factor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
positive regulation of ERK1 and ERK2 cascade ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of GTPase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of glucose import IEA
Inferred from Electronic Annotation
more info
 
positive regulation of neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of protein kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of vasculogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
protein localization to plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
regulation of cell junction assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of insulin secretion TAS
Traceable Author Statement
more info
 
regulation of neurotransmitter receptor localization to postsynaptic specialization membrane IDA
Inferred from Direct Assay
more info
PubMed 
regulation of neurotransmitter receptor localization to postsynaptic specialization membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to antineoplastic agent IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell IEA
Inferred from Electronic Annotation
more info
 
cell junction ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
early endosome ISS
Inferred from Sequence or Structural Similarity
more info
 
extracellular exosome HDA PubMed 
glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
guanyl-nucleotide exchange factor complex IEA
Inferred from Electronic Annotation
more info
 
late endosome ISS
Inferred from Sequence or Structural Similarity
more info
 
neuron projection IEA
Inferred from Electronic Annotation
more info
 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
phagocytic vesicle IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
specific granule membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
ras-related protein Rap-1A
Names
GTP-binding protein smg p21A
Ras-related protein Krev-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_001010935.2NP_001010935.1  ras-related protein Rap-1A precursor

    See identical proteins and their annotated locations for NP_001010935.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR, compared to variant 4. Variants 1-5 encode the same protein.
    Source sequence(s)
    AK094737, BC014086, BG743233, BI460853, BQ220294, BU167449, BU189979, BX473371, CA446565, DA102623, DB312010
    Consensus CDS
    CCDS840.1
    UniProtKB/Swiss-Prot
    P62834
    UniProtKB/TrEMBL
    A8KAH9
    Conserved Domains (1) summary
    cd04175
    Location:3167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms
  2. NM_001291896.1NP_001278825.1  ras-related protein Rap-1A precursor

    See identical proteins and their annotated locations for NP_001278825.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 4. Variants 1-5 encode the same protein.
    Source sequence(s)
    AK094737, AK293044, AL139012, BC014086, BG743233, BU167449, BU189979, BX473371, CA446565, DA102623, DB312010
    Consensus CDS
    CCDS840.1
    UniProtKB/Swiss-Prot
    P62834
    UniProtKB/TrEMBL
    A8KAH9
    Conserved Domains (1) summary
    cd04175
    Location:3167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms
  3. NM_001370216.1NP_001357145.1  ras-related protein Rap-1A precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) represents the longest transcript. Variants 1-5 encode the same protein.
    Source sequence(s)
    AL049557, AL390195
    Related
    ENSP00000348786.1, ENST00000356415.5
    Conserved Domains (1) summary
    cd04175
    Location:3167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms
  4. NM_001370217.1NP_001357146.1  ras-related protein Rap-1A precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 4. Variants 1-5 encode the same protein.
    Source sequence(s)
    AL049557
    Conserved Domains (1) summary
    cd04175
    Location:3167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms
  5. NM_002884.3NP_002875.1  ras-related protein Rap-1A precursor

    See identical proteins and their annotated locations for NP_002875.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 4. Variants 1-5 encode the same protein.
    Source sequence(s)
    AK094737, BC014086, BG743233, BI460853, BU167449, BU189979, BX473371, CA446565, CD108761, DA102623, DB312010
    Consensus CDS
    CCDS840.1
    UniProtKB/Swiss-Prot
    P62834
    UniProtKB/TrEMBL
    A8KAH9
    Related
    ENSP00000358723.3, ENST00000369709.3
    Conserved Domains (1) summary
    cd04175
    Location:3167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    111542009..111716695
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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