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

Gene ID: 66691, updated on 5-Mar-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, Apr 2022]
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. Chemical genetic screen identifies Gapex-5/GAPVD1 and STBD1 as novel AMPK substrates. Ducommun S, et al. Cell Signal, 2019 May. PMID 30772465
  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. Imaging of Rab5 activity identifies essential regulators for phagosome maturation. Kitano M, et al. Nature, 2008 May 8. PMID 18385674
  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 (28) 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
acts_upstream_of_or_within endocytosis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of GTPase activity 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
  
involved_in vesicle-mediated transport IEA
Inferred from Electronic Annotation
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 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

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