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    RAPGEF5 Rap guanine nucleotide exchange factor 5 [ Homo sapiens (human) ]

    Gene ID: 9771, updated on 2-Nov-2024

    Summary

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    Official Symbol
    RAPGEF5provided by HGNC
    Official Full Name
    Rap guanine nucleotide exchange factor 5provided by HGNC
    Primary source
    HGNC:HGNC:16862
    See related
    Ensembl:ENSG00000136237 MIM:609527; AllianceGenome:HGNC:16862
    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
    GFR; MRGEF; REPAC; MR-GEF
    Summary
    Members of the RAS (see HRAS; MIM 190020) subfamily of GTPases function in signal transduction as GTP/GDP-regulated switches that cycle between inactive GDP- and active GTP-bound states. Guanine nucleotide exchange factors (GEFs), such as RAPGEF5, serve as RAS activators by promoting acquisition of GTP to maintain the active GTP-bound state and are the key link between cell surface receptors and RAS activation (Rebhun et al., 2000 [PubMed 10934204]).[supplied by OMIM, Mar 2008]
    Expression
    Broad expression in brain (RPKM 18.5), spleen (RPKM 13.5) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RAPGEF5 in Genome Data Viewer
    Location:
    7p15.3
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (22118236..22357154, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (22254475..22493270, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (22157854..22396773, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene dynein axonemal heavy chain 11 Neighboring gene uncharacterized LOC107986775 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:21937780-21938979 Neighboring gene NANOG hESC enhancer GRCh37_chr7:21981192-21981812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:21985471-21986181 Neighboring gene cell division cycle associated 7 like Neighboring gene VISTA enhancer hs807 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22097966 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22117733 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22118756 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22119917 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22121421 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22123422 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22141595 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17999 Neighboring gene NANOG hESC enhancer GRCh37_chr7:22218362-22218864 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:22224198-22225096 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:22281835-22282335 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:22369304-22369804 Neighboring gene RNA, 5S ribosomal pseudogene 227 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25705 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18002 Neighboring gene HNF4 motif-containing MPRA enhancer 142 Neighboring gene GATA motif-containing MPRA enhancer 55/56 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:22517166-22517666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:22517667-22518167 Neighboring gene STEAP family member 1B Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 6

    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 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. Circ-RAPGEF5 promotes intrahepatic cholangiocarcinoma progression by stabilizing SAE1 to facilitate SUMOylation. Zheng J, et al. J Exp Clin Cancer Res, 2023 Sep 13. PMID 37705041, Free PMC Article
    2. Downregulation of circ-RAPGEF5 inhibits colorectal cancer progression by reducing the expression of polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3). Cheng D, et al. Environ Toxicol, 2024 Aug. PMID 38775215
    3. Characterization of GFR, a novel guanine nucleotide exchange factor for Rap1. Ichiba T, et al. FEBS Lett, 1999 Aug 20. PMID 10486569
    4. CircRAPGEF5 sponges miR-582-3p and targets KIF3A to regulate bladder cancer cell proliferation, migration and invasion. Wang C, et al. Int Immunopharmacol, 2024 Apr 20. PMID 38489970
    5. CircRNA cRAPGEF5 inhibits the growth and metastasis of renal cell carcinoma via the miR-27a-3p/TXNIP pathway. Chen Q, et al. Cancer Lett, 2020 Jan 28. PMID 31629934

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Downregulation of circ-RAPGEF5 inhibits colorectal cancer progression by reducing the expression of polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3).
      Title: Downregulation of circ-RAPGEF5 inhibits colorectal cancer progression by reducing the expression of polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3).
    2. CircRAPGEF5 sponges miR-582-3p and targets KIF3A to regulate bladder cancer cell proliferation, migration and invasion.
      Title: CircRAPGEF5 sponges miR-582-3p and targets KIF3A to regulate bladder cancer cell proliferation, migration and invasion.
    3. Circ-RAPGEF5 promotes intrahepatic cholangiocarcinoma progression by stabilizing SAE1 to facilitate SUMOylation.
      Title: Circ-RAPGEF5 promotes intrahepatic cholangiocarcinoma progression by stabilizing SAE1 to facilitate SUMOylation.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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
    A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study.
    EBI GWAS Catalog
    Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
    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

    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

    Clone Names

    • KIAA0277

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTP-dependent protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables guanyl-nucleotide exchange factor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Ras protein signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nervous system development NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in small GTPase-mediated signal transduction NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    rap guanine nucleotide exchange factor 5
    Names
    M-Ras-regulated GEF
    M-Ras-regulated Rap GEF
    Rap guanine nucleotide exchange factor (GEF) 5
    guanine nucleotide exchange factor for Rap1
    related to Epac

    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_001367600.2 → NP_001354529.1  rap guanine nucleotide exchange factor 5 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC005079
      Consensus CDS
      CCDS94064.1
      UniProtKB/Swiss-Prot
      A4D140, Q8IXU5, Q92565
      UniProtKB/TrEMBL
      A0A0S2Z561, B4DJ01
      Related
      ENSP00000384044.1, ENST00000401957.6

    2. NM_001367601.1 → NP_001354530.1  rap guanine nucleotide exchange factor 5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC005079
      UniProtKB/TrEMBL
      B4DJ01

    3. NM_001367602.2 → NP_001354531.1  rap guanine nucleotide exchange factor 5 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC005079

    4. NM_001367603.1 → NP_001354532.1  rap guanine nucleotide exchange factor 5 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC005079

    5. NM_012294.5 → NP_036426.4  rap guanine nucleotide exchange factor 5 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC005079
      Consensus CDS
      CCDS55093.2
      UniProtKB/TrEMBL
      A0A590UJR0, A8MQ07
      Related
      ENSP00000499535.1, ENST00000665637.1

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      22118236..22357154 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017012837.3 → XP_016868326.1  rap guanine nucleotide exchange factor 5 isoform X1

      UniProtKB/TrEMBL
      A8MQ07

    2. XM_047421084.1 → XP_047277040.1  rap guanine nucleotide exchange factor 5 isoform X2

    3. XM_047421083.1 → XP_047277039.1  rap guanine nucleotide exchange factor 5 isoform X2

    4. XM_011515652.3 → XP_011513954.1  rap guanine nucleotide exchange factor 5 isoform X2

      UniProtKB/TrEMBL
      B4DJ01
      Conserved Domains (2) summary
      smart00147
      Location:315 → 554
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
      smart00229
      Location:43 → 174
      RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      22254475..22493270 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359421.1 → XP_054215396.1  rap guanine nucleotide exchange factor 5 isoform X1

    2. XM_054359422.1 → XP_054215397.1  rap guanine nucleotide exchange factor 5 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92565.1 GenPept UniProtKB/Swiss-Prot:Q92565

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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