Rph3a rabphilin 3A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Rph3aprovided by RGD
Official Full Name: rabphilin 3Aprovided by RGD
Primary source: RGD:620073
See related: Ensembl:ENSRNOG00000001368 AllianceGenome:RGD:620073
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables several functions, including anion binding activity; calcium-dependent phospholipid binding activity; and metal ion binding activity. Involved in dendritic spine organization and regulation of NMDA receptor activity. Located in dendritic spine; postsynaptic membrane; and secretory vesicle. Is extrinsic component of membrane. Part of protein-containing complex. Is active in cholinergic synapse and neuromuscular junction. Is extrinsic component of synaptic vesicle membrane. Orthologous to human RPH3A (rabphilin 3A). [provided by Alliance of Genome Resources, Jul 2025]
Expression: Restricted expression toward (RPKM 215.8) See more
Orthologs: all
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Genomic context

Location:: 12q16

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	12	NC_086030.1 (41203004..41279536)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	12	NC_051347.1 (35542389..35618901)

Chromosome 12 - NC_086030.1 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Rabphilin 3A binds the N-peptide of SNAP-25 to promote SNARE complex assembly in exocytosis.
Title: Rabphilin 3A binds the N-peptide of SNAP-25 to promote SNARE complex assembly in exocytosis.
Rabphilin-3A Drives Structural Modifications of Dendritic Spines Induced by Long-Term Potentiation.
Title: Rabphilin-3A Drives Structural Modifications of Dendritic Spines Induced by Long-Term Potentiation.
Findings indicate that Rph3A activity is linked to the aberrant synaptic localization of GluN2A-expressing NMDARs characterizing levodopa-induced dyskinesias; suggest that Rph3A/GluN2A complex could represent an innovative therapeutic target for those pathological conditions where NMDAR composition is significantly altered.
Title: Rabphilin 3A: A novel target for the treatment of levodopa-induced dyskinesias.
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.
Interactions of SNAP25A and RPH3A take place at cell surface during stimulated exocytosis.
Title: In-depth fluorescence lifetime imaging analysis revealing SNAP25A-Rabphilin 3A interactions.
Structural determinants for Ca2+ and phosphatidylinositol 4,5-bisphosphate binding by the C2A domain of rabphilin-3A.
Title: Structural determinants for Ca2+ and phosphatidylinositol 4,5-bisphosphate binding by the C2A domain of rabphilin-3A.
different PIP2 headgroup recognition modes suggest that PIP2 is a target of the C2A domain of rabphilin-3A while this phospholipid is an effector of the C2B domain
Title: The PIP2 binding mode of the C2 domains of rabphilin-3A.
Three Rab3/27 effectors, Granuphilin, Noc2, and Rabphilin, in PC12 cells using fluorescence recovery after photobleaching of EGFP-tagged proteins.
Title: The Rab27 effector Rabphilin, unlike Granuphilin and Noc2, rapidly exchanges between secretory granules and cytosol in PC12 cells.
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.

Submit: New GeneRIF Correction See all GeneRIFs (15)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	TAS Traceable Author Statement more info	PubMed
enables calcium-dependent phospholipid binding	IDA Inferred from Direct Assay more info	PubMed
enables inositol 1,4,5 trisphosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphate ion binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol-4,5-bisphosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables phospholipid binding	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables selenium binding	IDA Inferred from Direct Assay more info	PubMed
enables small GTPase binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

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	IMP Inferred from Mutant Phenotype more info	PubMed
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
involved_in regulation of NMDA receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within spontaneous neurotransmitter secretion	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle priming	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cholinergic synapse	IDA Inferred from Direct Assay more info	PubMed
located_in dendritic spine	IDA Inferred from Direct Assay more info	PubMed
located_in dendritic spine	IEA Inferred from Electronic Annotation more info
located_in extrinsic component of membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in extrinsic component of synaptic vesicle membrane	EXP Inferred from Experiment more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
located_in extrinsic component of synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
is_active_in extrinsic component of synaptic vesicle membrane	IEP Inferred from Expression Pattern more info	PubMed
located_in membrane	EXP Inferred from Experiment more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in neuromuscular junction	IDA Inferred from Direct Assay more info	PubMed
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
is_active_in postsynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
located_in secretory granule	IDA Inferred from Direct Assay more info	PubMed
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: rabphilin-3A

Names: exophilin-1; rabphilin 3A homolog

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_001443856.1 → NP_001430785.1 rabphilin-3A isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000012

UniProtKB/Swiss-Prot

P47709
NM_133518.2 → NP_598202.2 rabphilin-3A isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000012

UniProtKB/Swiss-Prot

P47709

UniProtKB/TrEMBL

F1LPB9

Related

ENSRNOP00000001844.5, ENSRNOT00000001844.8

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

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

NC_086030.1 Reference GRCr8

Range

41203004..41279536

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006249379.5 → XP_006249441.1 rabphilin-3A isoform X1

UniProtKB/Swiss-Prot

P47709

UniProtKB/TrEMBL

F1LPB9

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_006249381.5 → XP_006249443.1 rabphilin-3A isoform X4

UniProtKB/TrEMBL

A0A8I6A3Z9

Related

ENSRNOP00000086545.2, ENSRNOT00000106706.2

Conserved Domains (3) summary

cd04035
Location:363 → 486

C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain

cd08384
Location:523 → 655

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
XM_039089039.2 → XP_038944967.1 rabphilin-3A isoform X5

UniProtKB/TrEMBL

A0ABK0LMS2

Related

ENSRNOP00000107113.1, ENSRNOT00000143871.1

Conserved Domains (4) summary

cd04035
Location:360 → 483

C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain

cd08384
Location:520 → 652

C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain

PHA03247
Location:158 → 329

PHA03247; large tegument protein UL36; Provisional

cd15762
Location:88 → 168

FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins
XM_006249380.5 → XP_006249442.1

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
XM_039089038.2 → XP_038944966.1 rabphilin-3A isoform X3

UniProtKB/Swiss-Prot

P47709

UniProtKB/TrEMBL

A0ABK0L3H9

Related

ENSRNOP00000103857.1, ENSRNOT00000151514.1

Conserved Domains (4) 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