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    Rapgef6 Rap guanine nucleotide exchange factor 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 303141, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Rapgef6provided by RGD
    Official Full Name
    Rap guanine nucleotide exchange factor 6provided by RGD
    Primary source
    RGD:1307645
    See related
    EnsemblRapid:ENSRNOG00000009995 AllianceGenome:RGD:1307645
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable several functions, including GTP-dependent protein binding activity; guanyl-nucleotide exchange factor activity; and phosphatidic acid binding activity. Predicted to be involved in several processes, including Ras protein signal transduction; microvillus assembly; and positive regulation of GTPase activity. Predicted to be located in centrosome and cytosol. Predicted to be active in apical plasma membrane and endocytic vesicle. Orthologous to human RAPGEF6 (Rap guanine nucleotide exchange factor 6). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 243.6), Spleen (RPKM 199.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rapgef6 in Genome Data Viewer
    Location:
    10q22
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (39156573..39324947)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (38655854..38824227)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (39875322..40039929)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene meiotic kinetochore factor Neighboring gene U6 spliceosomal RNA Neighboring gene folliculin interacting protein 1 Neighboring gene uncharacterized LOC134480793 Neighboring gene CDC42 small effector 2 Neighboring gene uncharacterized LOC120095101

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Identification and characterization of RA-GEF-2, a Rap guanine nucleotide exchange factor that serves as a downstream target of M-Ras. Gao X, et al. J Biol Chem, 2001 Nov 9. PMID 11524421
    2. JAM-A associates with ZO-2, afadin, and PDZ-GEF1 to activate Rap2c and regulate epithelial barrier function. Monteiro AC, et al. Mol Biol Cell, 2013 Sep. PMID 23885123, Free PMC Article
    3. Rap2A links intestinal cell polarity to brush border formation. Gloerich M, et al. Nat Cell Biol, 2012 Aug. PMID 22797597
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables GTP-dependent protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables guanyl-nucleotide exchange factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidic acid binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables small GTPase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in Ras protein signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    NOT involved_in establishment of endothelial intestinal barrier ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in microvillus assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of GTPase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization to plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in apical plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in apical plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in endocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endocytic vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    rap guanine nucleotide exchange factor 6
    Names
    Rap guanine nucleotide exchange factor (GEF) 6

    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_001107003.1 → NP_001100473.1  rap guanine nucleotide exchange factor 6

      See identical proteins and their annotated locations for NP_001100473.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473948
      UniProtKB/TrEMBL
      A0A8I5YCN5, A6HEI1
      Conserved Domains (7) summary
      smart00229
      Location:412 → 525
      RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
      COG0664
      Location:274 → 448
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      cd00038
      Location:280 → 380
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cd00155
      Location:857 → 1067
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
      cd00992
      Location:529 → 609
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cl00047
      Location:37 → 82
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cl00155
      Location:749 → 833
      UBQ; Ubiquitin-like proteins

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086028.1 Reference GRCr8

      Range
      39156573..39324947
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017597259.3 → XP_017452748.1  rap guanine nucleotide exchange factor 6 isoform X1

      UniProtKB/TrEMBL
      A0A8I5YCN5

    2. XM_006246279.4 → XP_006246341.1  rap guanine nucleotide exchange factor 6 isoform X5

      UniProtKB/TrEMBL
      A0A8I5YCN5
      Related
      ENSRNOP00000096908.2, ENSRNOT00000109709.2
      Conserved Domains (7) summary
      smart00229
      Location:412 → 525
      RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
      COG0664
      Location:274 → 448
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      cd00038
      Location:280 → 380
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cd00155
      Location:862 → 1086
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
      cd00992
      Location:529 → 609
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cl00047
      Location:37 → 82
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cl00155
      Location:754 → 838
      UBQ; Ubiquitin-like proteins

    3. XM_006246278.4 → XP_006246340.1  rap guanine nucleotide exchange factor 6 isoform X3

      UniProtKB/TrEMBL
      A0A8I5YCN5, D3ZTL8
      Related
      ENSRNOP00000090336.2, ENSRNOT00000099767.2
      Conserved Domains (7) summary
      smart00229
      Location:412 → 525
      RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
      COG0664
      Location:274 → 448
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      cd00038
      Location:280 → 380
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cd00155
      Location:862 → 1072
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
      cd00992
      Location:529 → 609
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cl00047
      Location:37 → 82
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cl00155
      Location:754 → 838
      UBQ; Ubiquitin-like proteins

    4. XM_063268981.1 → XP_063125051.1  rap guanine nucleotide exchange factor 6 isoform X7

      UniProtKB/TrEMBL
      A0A8I5YCN5

    5. XM_006246277.5 → XP_006246339.1  rap guanine nucleotide exchange factor 6 isoform X2

      UniProtKB/TrEMBL
      A0A8I5YCN5, A0A8I6GLT7
      Related
      ENSRNOP00000090946.2, ENSRNOT00000110844.2
      Conserved Domains (7) summary
      smart00229
      Location:412 → 525
      RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
      COG0664
      Location:274 → 448
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      cd00038
      Location:280 → 380
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cd00155
      Location:857 → 1081
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
      cd00992
      Location:529 → 609
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cl00047
      Location:37 → 82
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cl00155
      Location:749 → 833
      UBQ; Ubiquitin-like proteins

    6. XM_006246280.4 → XP_006246342.1  rap guanine nucleotide exchange factor 6 isoform X6

      UniProtKB/TrEMBL
      A0A8I5YCN5
      Conserved Domains (7) summary
      smart00229
      Location:412 → 525
      RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
      COG0664
      Location:274 → 448
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      cd00038
      Location:280 → 380
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cd00155
      Location:857 → 1081
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
      cd00992
      Location:529 → 609
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cl00047
      Location:37 → 82
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cl00155
      Location:749 → 833
      UBQ; Ubiquitin-like proteins

    7. XM_039085934.2 → XP_038941862.1  rap guanine nucleotide exchange factor 6 isoform X11

      Related
      ENSRNOP00000078181.2, ENSRNOT00000102938.2
      Conserved Domains (6) summary
      smart00229
      Location:412 → 525
      RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
      cd00038
      Location:280 → 380
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cd00155
      Location:862 → 1086
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
      cd00992
      Location:529 → 609
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd01785
      Location:756 → 838
      RA_PDZ-GEF1; Ras-associating (RA) domain found in PDZ domain-containing guanine nucleotide exchange factor 1 (PDZ-GEF1) and similar proteins
      cl00047
      Location:37 → 82
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

    8. XM_039085935.2 → XP_038941863.1  rap guanine nucleotide exchange factor 6 isoform X12

      Conserved Domains (6) summary
      smart00229
      Location:412 → 525
      RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
      cd00038
      Location:280 → 380
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cd00155
      Location:857 → 1067
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
      cd00992
      Location:529 → 609
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd01785
      Location:751 → 833
      RA_PDZ-GEF1; Ras-associating (RA) domain found in PDZ domain-containing guanine nucleotide exchange factor 1 (PDZ-GEF1) and similar proteins
      cl00047
      Location:37 → 82
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

    9. XM_017597260.2 → XP_017452749.1  rap guanine nucleotide exchange factor 6 isoform X4

      UniProtKB/TrEMBL
      A0A8I6AM01
      Related
      ENSRNOP00000094611.1, ENSRNOT00000113485.2

    10. XM_017597262.3 → XP_017452751.1  rap guanine nucleotide exchange factor 6 isoform X10

      UniProtKB/TrEMBL
      A0A8I5ZU25

    11. XM_017597261.3 → XP_017452750.1  rap guanine nucleotide exchange factor 6 isoform X8

      UniProtKB/TrEMBL
      A0A8I5ZU25

    12. XM_039085933.2 → XP_038941861.1  rap guanine nucleotide exchange factor 6 isoform X9

      UniProtKB/TrEMBL
      A0A8I5ZU25
      Conserved Domains (5) summary
      smart00229
      Location:265 → 378
      RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
      cd00038
      Location:133 → 233
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cd00155
      Location:710 → 934
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
      cd00992
      Location:382 → 462
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd01785
      Location:604 → 686
      RA_PDZ-GEF1; Ras-associating (RA) domain found in PDZ domain-containing guanine nucleotide exchange factor 1 (PDZ-GEF1) and similar proteins

    RNA

    1. XR_001840077.3 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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