Rab3d RAB3D, member RAS oncogene family [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rab3dprovided by MGI
Official Full Name: RAB3D, member RAS oncogene familyprovided by MGI
Primary source: MGI:MGI:97844
See related: Ensembl:ENSMUSG00000019066 AllianceGenome:MGI:97844
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: C130057E11Rik
Summary: Enables GTP-dependent protein binding activity. Acts upstream of or within peptidyl-cysteine methylation and regulation of exocytosis. Located in zymogen granule. Is expressed in epidermis; nervous system; pancreas; and retina. Orthologous to human RAB3D (RAB3D, member RAS oncogene family). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in colon adult (RPKM 51.1), stomach adult (RPKM 49.7) and 23 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9 A3; 9 7.91 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (21818787..21829623, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (21907491..21918199, complement)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data 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?

Alcohol-induced Golgiphagy is triggered by the downregulation of Golgi GTPase RAB3D.
Title: Alcohol-induced Golgiphagy is triggered by the downregulation of Golgi GTPase RAB3D.
MicroRNA-125a-5p modulates the proliferation and apoptosis of TM4 Sertoli cells by targeting RAB3D and regulating the PI3K/AKT signaling pathway.
Title: MicroRNA-125a-5p modulates the proliferation and apoptosis of TM4 Sertoli cells by targeting RAB3D and regulating the PI3K/AKT signaling pathway.
Loss of Rab3D from secretory vesicles, leading to disproportionate Rab27-to-Rab3D activity, may contribute to the enhanced release of cathepsin S in tears of patients with Sjogren's syndrome.
Title: Imbalanced Rab3D versus Rab27 increases cathepsin S secretion from lacrimal acini in a mouse model of Sjögren's Syndrome.
Data suggest that both microtubule-associated DYNLT (dynein light chain Tctex-type 1) and cytoplasmic DYNLT (dynein 1 intermediate chain 2 DYNC1LI2) are equally able to bind to small GTPases Rab3D (Rab3d GTPase) and RagA (Ras-related GTP binding A).
Title: DYNLT (Tctex-1) forms a tripartite complex with dynein intermediate chain and RagA, hence linking this small GTPase to the dynein motor.
Acute expression of Rab1 and Rab3d DN constructs partially alleviated this negative feedback mechanism and resulted in impaired ER to Golgi trafficking of procollagen.
Title: Rab GTPase mediated procollagen trafficking in ascorbic acid stimulated osteoblasts.
Targeted disruption of Tctex-1 by RNA interference significantly impairs bone resorption capacity and mislocalizes Rab3D vesicles in osteoclasts.
Title: Tctex-1, a novel interaction partner of Rab3D, is required for osteoclastic bone resorption.
MIST1 binds to highly conserved CATATG E-boxes to directly activate transcription of 6 genes, including those encoding the small GTPases RAB26 and RAB3D.
Title: RAB26 and RAB3D are direct transcriptional targets of MIST1 that regulate exocrine granule maturation.
Novel localization of pIgR to the regulated secretory pathway of lacrimal gland acinar cells and its secretion therefrom may be affected by its novel interaction with Rab3D.
Title: Direct interaction between Rab3D and the polymeric immunoglobulin receptor and trafficking through regulated secretory vesicles in lacrimal gland acinar cells.
Data suggest that Rab3D modulates a post-trans-Golgi network trafficking step that is required for osteoclastic bone resorption.
Title: Rab3D regulates a novel vesicular trafficking pathway that is required for osteoclastic bone resorption.
Rab3D has a role in binding GTP in pancreatic acini
Title: Dominant negative Rab3D mutants reduce GTP-bound endogenous Rab3D in pancreatic acini.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Variation

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Alleles

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

Endonuclease-mediated (2)
Gene trapped (1)
Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables GTP-dependent protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
enables GTPase activity	IEA Inferred from Electronic Annotation more info
enables myosin V binding	IBA Inferred from Biological aspect of Ancestor more info
enables myosin V binding	IEA Inferred from Electronic Annotation more info
enables myosin V binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in bone resorption	IEA Inferred from Electronic Annotation more info
involved_in exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in exocytosis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within peptidyl-cysteine methylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of regulated secretory pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of regulated secretory pathway	ISO Inferred from Sequence Orthology more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of exocytosis	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasmic microtubule	IEA Inferred from Electronic Annotation more info
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	HDA more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
is_active_in synaptic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in zymogen granule	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ras-related protein Rab-3D

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_001324531.1 → NP_001311460.1 ras-related protein Rab-3D

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice acceptor site in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.

Source sequence(s)

AK048395, AK169369, BQ033745

Consensus CDS

CCDS22912.1

UniProtKB/Swiss-Prot

P35276

UniProtKB/TrEMBL

Q543Q4

Related

ENSMUSP00000111008.4, ENSMUST00000115351.10

Conserved Domains (1) summary

cd01865
Location:22 → 186

Rab3; Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D
NM_031874.5 → NP_114080.2 ras-related protein Rab-3D

See identical proteins and their annotated locations for NP_114080.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.

Source sequence(s)

AK048395, AK169369, BQ033745, CN696618

Consensus CDS

CCDS22912.1

UniProtKB/Swiss-Prot

P35276

UniProtKB/TrEMBL

Q543Q4

Related

ENSMUSP00000113322.2, ENSMUST00000122211.8

Conserved Domains (1) summary

cd01865
Location:22 → 186

Rab3; Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D

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_000075.7 Reference GRCm39 C57BL/6J

Range

21818787..21829623 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011242423.4 → XP_011240725.1 ras-related protein Rab-3D isoform X1

See identical proteins and their annotated locations for XP_011240725.1

UniProtKB/Swiss-Prot

P35276

UniProtKB/TrEMBL

Q543Q4

Conserved Domains (1) summary

cd01865
Location:22 → 186

Rab3; Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D
XM_011242422.4 → XP_011240724.1 ras-related protein Rab-3D isoform X1

See identical proteins and their annotated locations for XP_011240724.1

UniProtKB/Swiss-Prot

P35276

UniProtKB/TrEMBL

Q543Q4

Conserved Domains (1) summary

cd01865
Location:22 → 186

Rab3; Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D