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

Summary

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. Involved in synaptic vesicle priming. Acts upstream of or within spontaneous neurotransmitter secretion. Predicted to be located in cytosol; dendritic spine; and secretory vesicle. Predicted to be extrinsic component of membrane. Predicted to be part of protein-containing complex. Predicted to be active in several cellular components, including cholinergic synapse; neuromuscular junction; and postsynaptic membrane. Predicted to be extrinsic component of synaptic vesicle membrane. 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, Nov 2024]
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

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_000071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
a possible role in glomerulopathies
Title: Glomerular podocytes possess the synaptic vesicle molecule Rab3A and its specific effector rabphilin-3a.
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.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW108370 (e-PCR)
- UniSTS:179249

AU022689 (e-PCR)
- UniSTS:207865

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables calcium ion binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables calcium-dependent phospholipid binding	ISO Inferred from Sequence Orthology more info
enables calcium-dependent phospholipid binding	ISS Inferred from Sequence or Structural Similarity more info
enables inositol 1,4,5 trisphosphate binding	ISO Inferred from Sequence Orthology more info
enables inositol 1,4,5 trisphosphate binding	ISS Inferred from Sequence or Structural Similarity more info
enables phosphate ion binding	ISO Inferred from Sequence Orthology more info
enables phosphate ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables phosphatidylinositol-4,5-bisphosphate binding	ISO Inferred from Sequence Orthology more info
enables phosphatidylinositol-4,5-bisphosphate binding	ISS Inferred from Sequence or Structural Similarity 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 protein-containing complex binding	ISS Inferred from Sequence or Structural Similarity more info
enables selenium binding	ISO Inferred from Sequence Orthology more info
enables selenium binding	ISS Inferred from Sequence or Structural Similarity more info
enables small GTPase binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in calcium-dependent activation of synaptic vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in dendritic spine organization	ISO Inferred from Sequence Orthology more info
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of calcium ion-dependent exocytosis	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
colocalizes_with Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cholinergic synapse	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic spine	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
located_in extrinsic component of membrane	ISS Inferred from Sequence or Structural Similarity 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
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 neuron projection	ISS Inferred from Sequence or Structural Similarity more info
is_active_in postsynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation 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
part_of protein-containing complex	ISS Inferred from Sequence or Structural Similarity more info
located_in secretory granule	ISO Inferred from Sequence Orthology more info
located_in secretory granule	ISS Inferred from Sequence or Structural Similarity more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in synapse	ISS Inferred from Sequence or Structural Similarity 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
located_in synaptic vesicle membrane	ISS Inferred from Sequence or Structural Similarity 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)

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

Status: VALIDATED

Source sequence(s)

AC015535
NM_001428999.1 → NP_001415928.1 rabphilin-3A isoform 3

Status: VALIDATED

Source sequence(s)

AC015535
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

NC_000071.7 Reference GRCm39 C57BL/6J

Range

121078562..121184249 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

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)
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
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
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