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

    Gene ID: 5906, updated on 9-Dec-2024

    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; 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
    NEW
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    Try the new Transcript table

    Genomic context

    See RAP1A in Genome Data Viewer
    Location:
    1p13.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (111542009..111716691)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (111556699..111731587)
    RS_2024_09 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 ATAC-STARR-seq lymphoblastoid active region 1498 Neighboring gene transmembrane and immunoglobulin domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1500 Neighboring gene adenosine A3 receptor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1501 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1505 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1506 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:112150779-112151472 Neighboring gene long intergenic non-protein coding RNA 1160 Neighboring gene uncharacterized LOC107985184 Neighboring gene Sharpr-MPRA regulatory region 155 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1186 Neighboring gene MPRA-validated peak362 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1187 Neighboring gene RNA, U6 small nuclear 151, pseudogene Neighboring gene keratin 18 pseudogene 57 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:112267545-112268314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1189 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1191 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1190 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1507 Neighboring gene uncharacterized LOC101928718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1508 Neighboring gene inka box actin regulator 2 Neighboring gene INKA2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1509 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:112298273-112299157 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

    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

    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

    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
     
    enables GTP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
     
    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
     
    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
     
    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
     
    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

    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)

    NEW Try the new Transcript table

    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_001010935.3NP_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, Q5U0C3
      Related
      ENSP00000509234.1, ENST00000687939.1
      Conserved Domains (1) summary
      cd04175
      Location:3167
      Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms
    2. NM_001291896.3NP_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, Q5U0C3
      Conserved Domains (1) summary
      cd04175
      Location:3167
      Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms
    3. NM_001370216.2NP_001357145.1  ras-related protein Rap-1A precursor

      Status: REVIEWED

      Source sequence(s)
      AL049557, AL390195
      Consensus CDS
      CCDS840.1
      UniProtKB/Swiss-Prot
      P10113, P62834
      UniProtKB/TrEMBL
      A8KAH9, Q5U0C3
      Related
      ENSP00000348786.1, ENST00000356415.5
      Conserved Domains (1) summary
      cd04175
      Location:3167
      Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms
    4. NM_001370217.2NP_001357146.1  ras-related protein Rap-1A precursor

      Status: REVIEWED

      Source sequence(s)
      AL049557, AL139012
      Consensus CDS
      CCDS840.1
      UniProtKB/Swiss-Prot
      P10113, P62834
      UniProtKB/TrEMBL
      A8KAH9, Q5U0C3
      Conserved Domains (1) summary
      cd04175
      Location:3167
      Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms
    5. NM_001394066.1NP_001380995.1  ras-related protein Rap-1A precursor

      Status: REVIEWED

      Source sequence(s)
      AL049557, AL139012
      Consensus CDS
      CCDS840.1
      UniProtKB/Swiss-Prot
      P10113, P62834
      UniProtKB/TrEMBL
      A8KAH9, Q5U0C3
      Conserved Domains (1) summary
      cd04175
      Location:3167
      Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms
    6. NM_002884.4NP_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, Q5U0C3
      Related
      ENSP00000358723.3, ENST00000369709.4
      Conserved Domains (1) summary
      cd04175
      Location:3167
      Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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)