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    Rph3a rabphilin 3A [ Mus musculus (house mouse) ]

    Gene ID: 19894, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Rph3aprovided by MGI
    Official Full Name
    rabphilin 3Aprovided by MGI
    Primary source
    MGI:MGI:102788
    See related
    Ensembl:ENSMUSG00000029608 AllianceGenome:MGI:102788
    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
    2900002P20Rik
    Summary
    Predicted to enable several functions, including anion binding activity; calcium-dependent phospholipid binding activity; and metal ion binding activity. Acts upstream of or within spontaneous neurotransmitter secretion. Predicted to be located in several cellular components, including dendritic spine; postsynaptic membrane; and secretory vesicle. Predicted to be extrinsic component of membrane. Predicted to be part of protein-containing complex. Predicted to colocalize with Golgi apparatus. Is expressed in hindbrain; medulla oblongata; and midbrain. Orthologous to human RPH3A (rabphilin 3A). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in cerebellum adult (RPKM 64.9), cortex adult (RPKM 57.6) and 4 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    5 F; 5 61.17 cM
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (121078562..121184249, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (120940499..121010116, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene 2'-5' oligoadenylate synthetase 1A Neighboring gene 2'-5' oligoadenylate synthetase 1 pseudogene Neighboring gene 2'-5' oligoadenylate synthetase 1D Neighboring gene predicted gene, 32185 Neighboring gene STARR-positive B cell enhancer ABC_E3611 Neighboring gene protein tyrosine phosphatase, non-receptor type 11 Neighboring gene STARR-positive B cell enhancer ABC_E4783 Neighboring gene STARR-positive B cell enhancer ABC_E6372 Neighboring gene predicted gene, 26205 Neighboring gene ribosomal protein L6

    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. Tyrosine phosphorylation of rabphilin during long-lasting long-term potentiation. Capron B, et al. Neurosci Lett, 2007 Mar 13. PMID 17223267
    2. Rabphilin3A reduces integrin-dependent growth cone signaling to restrict axon regeneration after trauma. Sekine Y, et al. Exp Neurol, 2022 Jul. PMID 35398339, Free PMC Article
    3. Depletion of rabphilin 3A in a transgenic mouse model (R6/1) of Huntington's disease, a possible culprit in synaptic dysfunction. Smith R, et al. Neurobiol Dis, 2005 Dec. PMID 15967669
    4. Rabphilin knock-out mice reveal that rabphilin is not required for rab3 function in regulating neurotransmitter release. Schlüter OM, et al. J Neurosci, 1999 Jul 15. PMID 10407024, Free PMC Article
    5. Leukocyte Cytoskeleton Polarization Is Initiated by Plasma Membrane Curvature from Cell Attachment. Ren C, et al. Dev Cell, 2019 Apr 22. PMID 30930167, Free PMC Article

    See all (58) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Ca(2+) sensor proteins in spontaneous release and synaptic plasticity: Limited contribution of Doc2c, rabphilin-3a and synaptotagmin 7 in hippocampal glutamatergic neurons.
      Title: Ca(2+) sensor proteins in spontaneous release and synaptic plasticity: Limited contribution of Doc2c, rabphilin-3a and synaptotagmin 7 in hippocampal glutamatergic neurons.
    2. Small GTPase ARF6 Is a Coincidence-Detection Code for RPH3A Polarization in Neutrophil Polarization.
      Title: Small GTPase ARF6 Is a Coincidence-Detection Code for RPH3A Polarization in Neutrophil Polarization.
    3. In mice, phosphorylation-regulated neutrophil polarization mechanism is driven by PKN1-mediated phosphorylation of a newly identified RAB21 effector RPH3A.
      Title: PKN1 Directs Polarized RAB21 Vesicle Trafficking via RPH3A and Is Important for Neutrophil Adhesion and Ischemia-Reperfusion Injury.
    4. Rph3A interacts with GluN2A and PSD-95 forming a complex that regulates NMDARs stabilization at postsynaptic membranes.
      Title: Rabphilin 3A retains NMDA receptors at synaptic sites through interaction with GluN2A/PSD-95 complex.
    5. Binding of rabphilin to SNAP-25 regulates exocytosis of synaptic vesicles after the readily releasable pool has either been physiologically exhausted by use-dependent depression, or has been artificially depleted by deletion of synaptobrevin.
      Title: Rabphilin regulates SNARE-dependent re-priming of synaptic vesicles for fusion.
    6. Our results indicate that a decrease in mRNA levels underlie the depletion of protein levels of rabphilin 3A, and we suggest that this reduction may be involved in causing impaired synaptic transmission in R6/1 mice.
      Title: Depletion of rabphilin 3A in a transgenic mouse model (R6/1) of Huntington's disease, a possible culprit in synaptic dysfunction.
    7. rabphilin, by interacting with alpha-actinin, organizes the cell cytoskeleton to facilitate granule localization within F-actin-rich regions
      Title: Rabphilin localizes with the cell actin cytoskeleton and stimulates association of granules with F-actin cross-linked by {alpha}-actinin.
    8. a possible role in glomerulopathies
      Title: Glomerular podocytes possess the synaptic vesicle molecule Rab3A and its specific effector rabphilin-3a.
    9. Our results suggest that rabphilin, a protein present in presynaptic terminals, could play a role in the late phase of L-LTP.
      Title: Tyrosine phosphorylation of rabphilin during long-lasting long-term potentiation.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (3)  1 citation
    • Endonuclease-mediated (4) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables calcium ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables calcium-dependent phospholipid binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables inositol 1,4,5 trisphosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables lipid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphate ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol-4,5-bisphosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables selenium binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables small GTPase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in dendritic spine organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of calcium ion-dependent exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spontaneous neurotransmitter secretion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within spontaneous neurotransmitter secretion IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in synaptic vesicle priming IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in synaptic vesicle priming IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cholinergic synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in dendritic spine ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extrinsic component of membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in extrinsic component of synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in extrinsic component of synaptic vesicle membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in neuromuscular junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in neuron projection IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in postsynaptic membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in postsynaptic membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in secretory granule ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synaptic vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in synaptic vesicle membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    rabphilin-3A
    Names
    Doc2 family
    exophilin-1

    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_001302344.2 → NP_001289273.1  rabphilin-3A isoform 1

      See identical proteins and their annotated locations for NP_001289273.1

      Status: VALIDATED

      Source sequence(s)
      AC015535
      Consensus CDS
      CCDS39246.1
      UniProtKB/Swiss-Prot
      P47708
      UniProtKB/TrEMBL
      Q768S5
      Related
      ENSMUSP00000143917.2, ENSMUST00000202406.4
      Conserved Domains (3) summary
      cd04035
      Location:380 → 503
      C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
      cd08384
      Location:540 → 672
      C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
      cd15762
      Location:88 → 168
      FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins

    2. NM_001302345.2 → NP_001289274.1  rabphilin-3A isoform 1

      See identical proteins and their annotated locations for NP_001289274.1

      Status: VALIDATED

      Source sequence(s)
      AC015535
      Consensus CDS
      CCDS39246.1
      UniProtKB/Swiss-Prot
      P47708
      UniProtKB/TrEMBL
      Q768S5
      Related
      ENSMUSP00000144291.2, ENSMUST00000202326.4
      Conserved Domains (3) summary
      cd04035
      Location:380 → 503
      C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
      cd08384
      Location:540 → 672
      C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
      cd15762
      Location:88 → 168
      FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins

    3. NM_001428998.1 → NP_001415927.1  rabphilin-3A isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC015535

    4. NM_001428999.1 → NP_001415928.1  rabphilin-3A isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC015535

    5. NM_011286.4 → NP_035416.1  rabphilin-3A isoform 1

      See identical proteins and their annotated locations for NP_035416.1

      Status: VALIDATED

      Source sequence(s)
      AC015535
      Consensus CDS
      CCDS39246.1
      UniProtKB/Swiss-Prot
      P47708
      UniProtKB/TrEMBL
      Q768S5
      Related
      ENSMUSP00000078198.6, ENSMUST00000079204.9
      Conserved Domains (3) summary
      cd04035
      Location:380 → 503
      C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
      cd08384
      Location:540 → 672
      C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
      cd15762
      Location:88 → 168
      FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins

    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_000071.7 Reference GRCm39 C57BL/6J

      Range
      121078562..121184249 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036164929.1 → XP_036020822.1  rabphilin-3A isoform X1

      UniProtKB/TrEMBL
      Q768S5
      Conserved Domains (4) summary
      cd04035
      Location:383 → 506
      C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
      cd08384
      Location:543 → 675
      C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
      PRK07764
      Location:175 → 352
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd15762
      Location:88 → 168
      FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins

    2. XM_036164928.1 → XP_036020821.1  rabphilin-3A isoform X1

      UniProtKB/TrEMBL
      Q768S5
      Conserved Domains (4) summary
      cd04035
      Location:383 → 506
      C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
      cd08384
      Location:543 → 675
      C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
      PRK07764
      Location:175 → 352
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd15762
      Location:88 → 168
      FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins

    3. XM_036164927.1 → XP_036020820.1  rabphilin-3A isoform X1

      UniProtKB/TrEMBL
      Q768S5
      Conserved Domains (4) summary
      cd04035
      Location:383 → 506
      C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
      cd08384
      Location:543 → 675
      C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
      PRK07764
      Location:175 → 352
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd15762
      Location:88 → 168
      FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins

    4. XM_011248186.4 → XP_011246488.1  rabphilin-3A isoform X1

      See identical proteins and their annotated locations for XP_011246488.1

      UniProtKB/TrEMBL
      Q768S5
      Conserved Domains (4) summary
      cd04035
      Location:383 → 506
      C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
      cd08384
      Location:543 → 675
      C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
      PRK07764
      Location:175 → 352
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd15762
      Location:88 → 168
      FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins

    5. XM_011248188.4 → XP_011246490.1  rabphilin-3A isoform X2

      UniProtKB/TrEMBL
      Q768S5
      Conserved Domains (5) summary
      cd04035
      Location:379 → 502
      C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
      cd08384
      Location:539 → 671
      C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
      PRK07764
      Location:171 → 348
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd15762
      Location:84 → 164
      FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins
      pfam03938
      Location:17 → 83
      OmpH; Outer membrane protein (OmpH-like)

    6. XM_036164931.1 → XP_036020824.1  rabphilin-3A isoform X3

      UniProtKB/TrEMBL
      Q768S5
      Conserved Domains (5) summary
      cd04035
      Location:376 → 499
      C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
      cd08384
      Location:536 → 668
      C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
      PRK07764
      Location:171 → 345
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd15762
      Location:84 → 164
      FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins
      pfam03938
      Location:17 → 83
      OmpH; Outer membrane protein (OmpH-like)

    7. XM_011248185.4 → XP_011246487.1  rabphilin-3A isoform X1

      See identical proteins and their annotated locations for XP_011246487.1

      UniProtKB/TrEMBL
      Q768S5
      Conserved Domains (4) summary
      cd04035
      Location:383 → 506
      C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
      cd08384
      Location:543 → 675
      C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
      PRK07764
      Location:175 → 352
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd15762
      Location:88 → 168
      FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins

    8. XM_011248187.4 → XP_011246489.1  rabphilin-3A isoform X1

      See identical proteins and their annotated locations for XP_011246489.1

      UniProtKB/TrEMBL
      Q768S5
      Conserved Domains (4) summary
      cd04035
      Location:383 → 506
      C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
      cd08384
      Location:543 → 675
      C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
      PRK07764
      Location:175 → 352
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd15762
      Location:88 → 168
      FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins

    9. XM_036164930.1 → XP_036020823.1  rabphilin-3A isoform X1

      UniProtKB/TrEMBL
      Q768S5
      Conserved Domains (4) summary
      cd04035
      Location:383 → 506
      C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
      cd08384
      Location:543 → 675
      C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
      PRK07764
      Location:175 → 352
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd15762
      Location:88 → 168
      FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P47708.2 GenPept UniProtKB/Swiss-Prot:P47708

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