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    Gapvd1 GTPase activating protein and VPS9 domains 1 [ Mus musculus (house mouse) ]

    Gene ID: 66691, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Gapvd1provided by MGI
    Official Full Name
    GTPase activating protein and VPS9 domains 1provided by MGI
    Primary source
    MGI:MGI:1913941
    See related
    Ensembl:ENSMUSG00000026867 AllianceGenome:MGI:1913941
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    RAP6; RME-6; Gapex-5; mKIAA1521; 2010005B09Rik; 4432404J10Rik
    Summary
    Enables GTPase activating protein binding activity and guanyl-nucleotide exchange factor activity. Involved in regulation of protein transport. Located in cytosol. Is expressed in several structures, including gonad; inner ear; nervous system; nucleus pulposus; and thymus primordium. Orthologous to human GAPVD1 (GTPase activating protein and VPS9 domains 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in CNS E14 (RPKM 8.3), liver E14 (RPKM 7.9) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Gapvd1 in Genome Data Viewer
    Location:
    2 B; 2 22.87 cM
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (34566190..34645297, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (34676178..34755285, complement)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase associated protein 1 Neighboring gene predicted gene, 34178 Neighboring gene ribosomal protein S3A pseudogene Neighboring gene STARR-seq mESC enhancer starr_04261 Neighboring gene STARR-positive B cell enhancer mm9_chr2:34501857-34502157 Neighboring gene predicted gene, 34372 Neighboring gene DnaJ (Hsp40) homolog, subfamily B, member 6 pseudogene Neighboring gene STARR-seq mESC enhancer starr_04265 Neighboring gene Rab9 effector protein with kelch motifs Neighboring gene predicted gene, 53241 Neighboring gene heat shock protein 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Imaging of Rab5 activity identifies essential regulators for phagosome maturation. Kitano M, et al. Nature, 2008 May 8. PMID 18385674
    2. Insulin stimulates phosphatidylinositol 3-phosphate production via the activation of Rab5. Lodhi IJ, et al. Mol Biol Cell, 2008 Jul. PMID 18434594, Free PMC Article
    3. Chemical genetic screen identifies Gapex-5/GAPVD1 and STBD1 as novel AMPK substrates. Ducommun S, et al. Cell Signal, 2019 May. PMID 30772465
    4. Gapex-5, a Rab31 guanine nucleotide exchange factor that regulates Glut4 trafficking in adipocytes. Lodhi IJ, et al. Cell Metab, 2007 Jan. PMID 17189207, Free PMC Article
    5. Rab22B is expressed in the CNS astroglia lineage and plays a role in epidermal growth factor receptor trafficking in A431 cells. Ng EL, et al. J Cell Physiol, 2009 Dec. PMID 19725050

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. AMPK-dependent phosphorylation of Gapex-5 (also known as GTPase-activating protein and VPS9 domain-containing protein 1 (GAPVD1)) on Ser902 in hepatocytes and starch-binding domain 1 (STBD1) on Ser175 in multiple cells/tissues
      Title: Chemical genetic screen identifies Gapex-5/GAPVD1 and STBD1 as novel AMPK substrates.
    2. the TC10/GAPEX-5/Rab5 axis mediates insulin-stimulated production of PI(3)P, which regulates trafficking of Glut4 vesicles
      Title: Insulin stimulates phosphatidylinositol 3-phosphate production via the activation of Rab5.
    3. Insulin recruits the CIP4/Gapex-5 complex to the plasma membrane, thus reducing Rab31 activity and permitting Glut4 vesicles to translocate to the cell surface, where Glut4 docks and fuses to transport glucose into the cell.
      Title: Gapex-5, a Rab31 guanine nucleotide exchange factor that regulates Glut4 trafficking in adipocytes.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 

    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

    • KIAA1521

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables GTPase activating protein binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables GTPase activating protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables GTPase activator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables guanyl-nucleotide exchange factor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables guanyl-nucleotide exchange factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in endocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of protein transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of protein transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    GTPase-activating protein and VPS9 domain-containing protein 1
    Names
    rab5-activating protein 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_001356441.1 → NP_001343370.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL845262, AL929106
      Consensus CDS
      CCDS89478.1
      UniProtKB/Swiss-Prot
      A0PJI8, A2AR09, A2AR10, A2AR17, A2AR18, Q3TNS1, Q3UDL0, Q3UYD5, Q6PAR5, Q6ZPP0, Q80V37, Q80ZK4, Q8BTS5, Q9CRS2, Q9CTI1
      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1354 → 1455
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1243 → 1306
      DUF5601; Domain of unknown function (DUF5601)

    2. NM_025709.3 → NP_079985.2  GTPase-activating protein and VPS9 domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_079985.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AL845262, BC060123
      Consensus CDS
      CCDS15949.1
      UniProtKB/Swiss-Prot
      Q6PAR5
      Related
      ENSMUSP00000099864.2, ENSMUST00000102800.9
      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1333 → 1434
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1222 → 1285
      DUF5601; Domain of unknown function (DUF5601)

    RNA

    1. NR_151469.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate exon, lacks another alternate exon, and uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL845262, AL929106

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      34566190..34645297 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011239150.3 → XP_011237452.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X7

      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1327 → 1428
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1216 → 1279
      DUF5601; Domain of unknown function (DUF5601)

    2. XM_036162467.1 → XP_036018360.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X3

      UniProtKB/Swiss-Prot
      A0PJI8, A2AR09, A2AR10, A2AR17, A2AR18, Q3TNS1, Q3UDL0, Q3UYD5, Q6PAR5, Q6ZPP0, Q80V37, Q80ZK4, Q8BTS5, Q9CRS2, Q9CTI1
      Related
      ENSMUSP00000108723.4, ENSMUST00000113099.10
      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1354 → 1455
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1243 → 1306
      DUF5601; Domain of unknown function (DUF5601)

    3. XM_036162475.1 → XP_036018368.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X7

      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1327 → 1428
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1216 → 1279
      DUF5601; Domain of unknown function (DUF5601)

    4. XM_017319197.2 → XP_017174686.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X9

      UniProtKB/TrEMBL
      F7ADQ2
      Conserved Domains (2) summary
      pfam02204
      Location:717 → 818
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:606 → 669
      DUF5601; Domain of unknown function (DUF5601)

    5. XM_036162477.1 → XP_036018370.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X10

      UniProtKB/TrEMBL
      F7ADQ2
      Related
      ENSMUSP00000108735.2, ENSMUST00000113111.8
      Conserved Domains (2) summary
      pfam02204
      Location:690 → 791
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:579 → 642
      DUF5601; Domain of unknown function (DUF5601)

    6. XM_017319195.3 → XP_017174684.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X1

      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1381 → 1482
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1270 → 1333
      DUF5601; Domain of unknown function (DUF5601)

    7. XM_030251955.2 → XP_030107815.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X4

      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1354 → 1455
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1243 → 1306
      DUF5601; Domain of unknown function (DUF5601)

    8. XM_036162476.1 → XP_036018369.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X8

      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1306 → 1407
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1195 → 1258
      DUF5601; Domain of unknown function (DUF5601)

    9. XM_036162472.1 → XP_036018365.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X6

      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1333 → 1434
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1222 → 1285
      DUF5601; Domain of unknown function (DUF5601)

    10. XM_030251954.2 → XP_030107814.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X2

      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1360 → 1461
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1249 → 1312
      DUF5601; Domain of unknown function (DUF5601)

    11. XM_036162470.1 → XP_036018363.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X5

      Related
      ENSMUSP00000028224.9, ENSMUST00000028224.15
      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1333 → 1434
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1222 → 1285
      DUF5601; Domain of unknown function (DUF5601)

    12. XM_017319196.3 → XP_017174685.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X1

      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1381 → 1482
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1270 → 1333
      DUF5601; Domain of unknown function (DUF5601)

    13. XM_036162478.1 → XP_036018371.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X13

      UniProtKB/TrEMBL
      F7ADT6
      Related
      ENSMUSP00000108725.2, ENSMUST00000113101.8
      Conserved Domains (2) summary
      pfam02204
      Location:551 → 652
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:440 → 503
      DUF5601; Domain of unknown function (DUF5601)

    14. XM_036162473.1 → XP_036018366.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X7

      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1327 → 1428
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1216 → 1279
      DUF5601; Domain of unknown function (DUF5601)

    15. XM_036162468.1 → XP_036018361.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X3

      UniProtKB/Swiss-Prot
      A0PJI8, A2AR09, A2AR10, A2AR17, A2AR18, Q3TNS1, Q3UDL0, Q3UYD5, Q6PAR5, Q6ZPP0, Q80V37, Q80ZK4, Q8BTS5, Q9CRS2, Q9CTI1
      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1354 → 1455
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1243 → 1306
      DUF5601; Domain of unknown function (DUF5601)

    16. XM_036162471.1 → XP_036018364.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X5

      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1333 → 1434
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1222 → 1285
      DUF5601; Domain of unknown function (DUF5601)

    17. XM_036162465.1 → XP_036018358.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X1

      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1381 → 1482
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1270 → 1333
      DUF5601; Domain of unknown function (DUF5601)

    18. XM_036162469.1 → XP_036018362.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X3

      UniProtKB/Swiss-Prot
      A0PJI8, A2AR09, A2AR10, A2AR17, A2AR18, Q3TNS1, Q3UDL0, Q3UYD5, Q6PAR5, Q6ZPP0, Q80V37, Q80ZK4, Q8BTS5, Q9CRS2, Q9CTI1
      Conserved Domains (3) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6
      pfam02204
      Location:1354 → 1455
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:1243 → 1306
      DUF5601; Domain of unknown function (DUF5601)

    19. XM_036162479.1 → XP_036018372.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X13

      UniProtKB/TrEMBL
      F7ADT6
      Conserved Domains (2) summary
      pfam02204
      Location:551 → 652
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:440 → 503
      DUF5601; Domain of unknown function (DUF5601)

    20. XM_036162482.1 → XP_036018375.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X15

      Conserved Domains (1) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6

    21. XM_030251957.2 → XP_030107817.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X11

      Conserved Domains (1) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6

    22. XM_036162481.1 → XP_036018374.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X14

      Conserved Domains (1) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6

    23. XM_030251958.2 → XP_030107818.1  GTPase-activating protein and VPS9 domain-containing protein 1 isoform X12

      Conserved Domains (1) summary
      cd05129
      Location:84 → 449
      RasGAP_RAP6; Ras-GTPase Activating Domain of Rab5-activating protein 6

    RNA

    1. XR_004940698.1 RNA Sequence

    2. XR_004940697.1 RNA Sequence

    3. XR_003953694.2 RNA Sequence

    4. XR_003953693.2 RNA Sequence

    5. XR_003953692.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6PAR5.2 GenPept UniProtKB/Swiss-Prot:Q6PAR5

    Gene LinkOut

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