Rabgef1 RAB guanine nucleotide exchange factor (GEF) 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rabgef1provided by MGI
Official Full Name: RAB guanine nucleotide exchange factor (GEF) 1provided by MGI
Primary source: MGI:MGI:1929459
See related: Ensembl:ENSMUSG00000025340 AllianceGenome:MGI:1929459
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: Rin2; Rab5ef; Rabex5
Summary: Enables ubiquitin protein ligase activity. Acts upstream of or within several processes, including negative regulation of macromolecule metabolic process; regulation of signal transduction; and regulation of vesicle-mediated transport. Located in vesicle. Is expressed in genitourinary system; hippocampus; and retina nuclear layer. Orthologous to human RABGEF1 (RAB guanine nucleotide exchange factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in bladder adult (RPKM 13.1), CNS E18 (RPKM 5.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 5; 5 G1.3

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	5	NC_000071.7 (130200644..130243178)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	5	NC_000071.6 (130171819..130214342)

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?

Loss of endocytosis-associated RabGEF1 causes aberrant morphogenesis and altered autophagy in photoreceptors leading to retinal degeneration.
Title: Loss of endocytosis-associated RabGEF1 causes aberrant morphogenesis and altered autophagy in photoreceptors leading to retinal degeneration.
Epithelial RABGEF1 deficiency promotes intestinal inflammation by dysregulating intrinsic MYD88-dependent innate signaling.
Title: Epithelial RABGEF1 deficiency promotes intestinal inflammation by dysregulating intrinsic MYD88-dependent innate signaling.
AP-1/sigma1A-ArfGAP1-Rabex-5 complex formation leads to more endosomal Rabex-5 and enhanced, Rab5(GTP)-stimulated Vps34 PI3-kinase activity, which is essential for multivesicular body endosome formation.
Title: AP-1/σ1A and AP-1/σ1B adaptor-proteins differentially regulate neuronal early endosome maturation via the Rab5/Vps34-pathway.
findings reveal a key role for RABGEF1 in dampening keratinocyte-intrinsic MYD88 signaling and sustaining epidermal barrier function
Title: Guanine nucleotide exchange factor RABGEF1 regulates keratinocyte-intrinsic signaling to maintain skin homeostasis.
Knockdown of RABEX-5 also inhibited wound healing, migration and the invasive abilities of gastric cancer cells.
Title: RABEX-5 is upregulated and plays an oncogenic role in gastric cancer development by activating the VEGF signaling pathway.
Hyperinsulinemia induced insulin resistance in 3T3-L1 adipocytes by retaining GLUT4 in a Rab5-activity-dependent compartment.
Title: Rab5 activity regulates GLUT4 sorting into insulin-responsive and non-insulin-responsive endosomal compartments: a potential mechanism for development of insulin resistance.
Kruppel-like factor 5 is indispensable for adhesion, homing, lodging and retention of haematopoietic stem cells and progenitors in the bone marrow through Rab5-dependent post-translational regulation of beta1/beta2 integrins
Title: Klf5 controls bone marrow homing of stem cells and progenitors through Rab5-mediated β1/β2-integrin trafficking.
Rab5 is required for phagocytosis of heat-inactivated Pseudomonas aeruginosa by macrophages.
Title: Regulation of Rab5 function during phagocytosis of live Pseudomonas aeruginosa in macrophages.
Rabex-5 regulates neurite morphogenesis of hippocampal neurons by activating at least two downstream targets, Rab5, which is localized in both axons and dendrites, and Rab17, which is localized in dendrites alone
Title: Rabex-5 protein regulates dendritic localization of small GTPase Rab17 and neurite morphogenesis in hippocampal neurons.
a novel mechanistic insight into how Rabex-5 regulates internalization and postendocytic trafficking of ubiquitinated L1 destined for lysosomal degradation.
Title: Rabex-5 protein regulates the endocytic trafficking pathway of ubiquitinated neural cell adhesion molecule L1.

Submit: New GeneRIF Correction See all GeneRIFs (19)

Variation

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Alleles

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

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Homologs of the Rabgef1 gene: The Rabgef1 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, zebrafish, fruit fly, mosquito, C.elegans, and rice.
Orthologs from Annotation Pipeline: 329 organisms have orthologs with human gene Rabgef1
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables guanyl-nucleotide exchange factor activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables guanyl-nucleotide exchange factor activity	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation 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	PubMed
enables small GTPase binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of Kit signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of Ras protein signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in dendritic transport	IDA Inferred from Direct Assay more info	PubMed
involved_in dendritic transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in dendritic transport	IPI Inferred from Physical Interaction more info	PubMed
acts_upstream_of_or_within endocytosis	IEA Inferred from Electronic Annotation more info
acts_upstream_of establishment of localization in cell	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of interleukin-6 production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of mast cell cytokine production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of mast cell degranulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of mast cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of Kit signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of Ras protein signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of inflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of interleukin-6 production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of leukocyte migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of mast cell activation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of mast cell cytokine production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of mast cell degranulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of receptor-mediated endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein targeting to membrane	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of receptor-mediated endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of Fc receptor mediated stimulatory signaling pathway	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of Fc receptor mediated stimulatory signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle-mediated transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in dendrite	IPI Inferred from Physical Interaction more info	PubMed
located_in early endosome	ISO Inferred from Sequence Orthology more info
is_active_in endocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in vesicle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: rab5 GDP/GTP exchange factor

Names: Rab5 exchange factor; Ras negative regulator Rabex-5; Ras negative regulator Rabex-5/Rin2; rabex-5

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_001199059.2 → NP_001185988.1 rab5 GDP/GTP exchange factor isoform a

See identical proteins and their annotated locations for NP_001185988.1

Status: VALIDATED

Source sequence(s)

AC113029, AC122339

Consensus CDS

CCDS19708.1

UniProtKB/Swiss-Prot

Q3UIW0, Q9JM13

Related

ENSMUSP00000114103.2, ENSMUST00000119797.8

Conserved Domains (2) summary

pfam01754
Location:17 → 40

zf-A20; A20-like zinc finger

pfam02204
Location:270 → 370

VPS9; Vacuolar sorting protein 9 (VPS9) domain
NM_001359233.2 → NP_001346162.1 rab5 GDP/GTP exchange factor isoform b

Status: VALIDATED

Source sequence(s)

AC113029, AC122339

Conserved Domains (1) summary

pfam02204
Location:78 → 178

VPS9; Vacuolar sorting protein 9 (VPS9) domain
NM_001378873.1 → NP_001365802.1 rab5 GDP/GTP exchange factor isoform c

Status: VALIDATED

Source sequence(s)

AC113029, AC122339

UniProtKB/TrEMBL

A0A8C6HQW3

Conserved Domains (3) summary

pfam02204
Location:271 → 371

VPS9; Vacuolar sorting protein 9 (VPS9) domain

pfam01754
Location:17 → 39

zf-A20; A20-like zinc finger

pfam18151
Location:159 → 221

DUF5601; Domain of unknown function (DUF5601)
NM_001403280.1 → NP_001390209.1 rab5 GDP/GTP exchange factor isoform a

Status: VALIDATED

Source sequence(s)

AC113029, AC122339

UniProtKB/Swiss-Prot

Q3UIW0
NM_001403281.1 → NP_001390210.1 rab5 GDP/GTP exchange factor isoform b

Status: VALIDATED

Source sequence(s)

AC113029, AC122339
NM_001403282.1 → NP_001390211.1 rab5 GDP/GTP exchange factor isoform c

Status: VALIDATED

Source sequence(s)

AC113029, AC122339

UniProtKB/TrEMBL

A0A8C6HQW3
NM_001403283.1 → NP_001390212.1 rab5 GDP/GTP exchange factor isoform c

Status: VALIDATED

Source sequence(s)

AC113029, AC122339

UniProtKB/TrEMBL

A0A8C6HQW3
NM_019983.3 → NP_064367.1 rab5 GDP/GTP exchange factor isoform a

See identical proteins and their annotated locations for NP_064367.1

Status: VALIDATED

Source sequence(s)

AC113029, AC122339

Consensus CDS

CCDS19708.1

UniProtKB/Swiss-Prot

Q3UIW0, Q9JM13

Related

ENSMUSP00000026390.8, ENSMUST00000026390.8

Conserved Domains (2) summary

pfam01754
Location:17 → 40

zf-A20; A20-like zinc finger

pfam02204
Location:270 → 370

VPS9; Vacuolar sorting protein 9 (VPS9) domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

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

130200644..130243178

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036165356.1 → XP_036021249.1 rab5 GDP/GTP exchange factor isoform X3

Conserved Domains (1) summary

pfam02204
Location:63 → 163

VPS9; Vacuolar sorting protein 9 (VPS9) domain
XM_036165358.1 → XP_036021251.1 rab5 GDP/GTP exchange factor isoform X3

Conserved Domains (1) summary

pfam02204
Location:63 → 163

VPS9; Vacuolar sorting protein 9 (VPS9) domain
XM_006504446.5 → XP_006504509.1 rab5 GDP/GTP exchange factor isoform X1

Conserved Domains (3) summary

pfam01754
Location:35 → 58

zf-A20; A20-like zinc finger

pfam02204
Location:289 → 389

VPS9; Vacuolar sorting protein 9 (VPS9) domain

pfam18151
Location:177 → 239

DUF5601; Domain of unknown function (DUF5601)
XM_006504447.4 → XP_006504510.1 rab5 GDP/GTP exchange factor isoform X2

Conserved Domains (3) summary

pfam01754
Location:35 → 58

zf-A20; A20-like zinc finger

pfam02204
Location:288 → 388

VPS9; Vacuolar sorting protein 9 (VPS9) domain

pfam18151
Location:176 → 238

DUF5601; Domain of unknown function (DUF5601)