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

Gene ID: 9771, updated on 10-Dec-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
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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
  • 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)

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

    UniProtKB/TrEMBL
    B4DJ01

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

    UniProtKB/TrEMBL
    B4DJ01

  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

    UniProtKB/TrEMBL
    A8MQ07

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

    UniProtKB/TrEMBL
    B4DJ01
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92565.1 GenPept UniProtKB/Swiss-Prot:Q92565

Gene LinkOut

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