Rabep1 rabaptin, RAB GTPase binding effector protein 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rabep1provided by MGI
Official Full Name: rabaptin, RAB GTPase binding effector protein 1provided by MGI
Primary source: MGI:MGI:1860236
See related: Ensembl:ENSMUSG00000020817 AllianceGenome:MGI:1860236
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: Rab5ep; rabaptin-5; rabaptin-5alpha
Summary: Predicted to enable protein domain specific binding activity and protein homodimerization activity. Involved in Golgi to plasma membrane transport and protein localization to ciliary membrane. Located in endosome. Is expressed in brain; embryo; head; lung; and thymus. Orthologous to human RABEP1 (rabaptin, RAB GTPase binding effector protein 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in adrenal adult (RPKM 21.5), CNS E18 (RPKM 11.5) and 26 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 B3- B4; 11 43.21 cM

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (70735553..70833931)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (70844724..70943105)

Chromosome 11 - NC_000077.7 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?

The RabGEF ALS2 is a hypoxia inducible target associated with the acquisition of aggressive traits in tumor cells.
Title: The RabGEF ALS2 is a hypoxia inducible target associated with the acquisition of aggressive traits in tumor cells.
Restoring C9ORF72 levels or augmenting its function with constitutively active RAB5 or chemical modulators of RAB5 effectors rescued patient neuron survival and ameliorated neurodegenerative processes in both gain- and loss-of-function C9ORF72 mouse models
Title: Haploinsufficiency leads to neurodegeneration in C9ORF72 ALS/FTD human induced motor neurons.
novel protein complex composed of Rabep1, GGA1 and Arl3 is responsible for the sorting and targeting of the polycystin 1 andpolycystin 2 to the cilium.
Title: Ciliary membrane proteins traffic through the Golgi via a Rabep1/GGA1/Arl3-dependent mechanism.
The intracellular localization of Rabaptin-5gamma indicates that it is not involved in Rab5-driven events--rather, it functions in other membrane transport steps; role of alternative splicing in determination of functional activities of Rab effector molecules
Title: Characterization of Rabaptin-5 γ isoform.
our results assign Rab5 a key role in mediating mast cell secretory granule fusion during biogenesis
Title: Rab5 is a novel regulator of mast cell secretory granules: impact on size, cargo, and exocytosis.
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.
The disruption of Rabaptin-5 Ser407 phosphorylation reduces persistent cell migration in 2D and alphavbeta3-dependent invasion.
Title: PKD controls αvβ3 integrin recycling and tumor cell invasive migration through its substrate Rabaptin-5.
Data reveal the affinity of Rabex-5/Rabaptin-5/Rab5-GTP interaction in the cell, which is quantitatively related to the Rabex-5 concentration for the onset of the indirect positive feedback pathway.
Title: Delayed onset of positive feedback activation of Rab5 by Rabex-5 and Rabaptin-5 in endocytosis.
Rabaptin-5 importantly contributes to mast cell IgE-dependent immunologic function by enhancing mast cell receptor surface stability.
Title: Rabaptin-5 regulates receptor expression and functional activation in mast cells.
Western blot analysis of the mouse brain showed reduced levels of calpastatin and rabaptin-5 and higher amount of neuronatin in PKU compared to the wild type.
Title: Expression of calpastatin, minopontin, NIPSNAP1, rabaptin-5 and neuronatin in the phenylketonuria (PKU) mouse brain: possible role on cognitive defect seen in PKU.

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Variation

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Alleles

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

Gene trapped (1)
Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AV213537 (e-PCR)
- UniSTS:180242

D11Die10 (e-PCR), detects polymorphism
- UniSTS:226092

RH124505 (e-PCR)
- UniSTS:161327

RH125884 (e-PCR)
- UniSTS:162616

D11Die31 (e-PCR), detects polymorphism
- UniSTS:226106

Rabep1 (e-PCR), detects polymorphism
- UniSTS:259398

Rabep1 (e-PCR), detects polymorphism
- UniSTS:259399

D11Die9 (e-PCR), detects polymorphism
- UniSTS:226120

NoName (e-PCR)
- UniSTS:236626

AI481320 (e-PCR)
- UniSTS:160116

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables GTPase activator activity	IEA Inferred from Electronic Annotation more info
enables growth factor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in Golgi to plasma membrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in Golgi to plasma membrane transport	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within endocytosis	IEA Inferred from Electronic Annotation more info
involved_in endocytosis	IEA Inferred from Electronic Annotation more info
involved_in protein localization to ciliary membrane	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of postsynaptic neurotransmitter receptor internalization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of postsynaptic neurotransmitter receptor internalization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle-mediated transport	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic vesicle	IEA Inferred from Electronic Annotation more info
is_active_in endocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in endocytic vesicle	ISO Inferred from Sequence Orthology more info
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic cytosol	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: rab GTPase-binding effector protein 1

Names: RAB5 effector protein; neurocrescin; rabaptin 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_001291141.1 → NP_001278070.1 rab GTPase-binding effector protein 1 isoform 2

See identical proteins and their annotated locations for NP_001278070.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

AK134587, BC060166, BC080274, BY133091

Consensus CDS

CCDS70232.1

UniProtKB/Swiss-Prot

O35551

Related

ENSMUSP00000137267.2, ENSMUST00000178245.2

Conserved Domains (3) summary

pfam03528
Location:11 → 452

Rabaptin; Rabaptin

pfam09311
Location:490 → 796

Rab5-bind; Rabaptin-like protein

pfam10267
Location:605 → 741

Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein
NM_001291142.1 → NP_001278071.1 rab GTPase-binding effector protein 1 isoform 3

See identical proteins and their annotated locations for NP_001278071.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.

Source sequence(s)

AK134587, BC060166, BC080274, BY133091

Consensus CDS

CCDS78984.1

UniProtKB/Swiss-Prot

O35551

Related

ENSMUSP00000080102.7, ENSMUST00000081362.13

Conserved Domains (4) summary

pfam03528
Location:9 → 455

Rabaptin; Rabaptin

pfam09311
Location:493 → 799

Rab5-bind; Rabaptin-like protein

pfam10267
Location:608 → 744

Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein

cl14813
Location:26 → 157

GluZincin; Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins)
NM_001291143.1 → NP_001278072.1 rab GTPase-binding effector protein 1 isoform 4

See identical proteins and their annotated locations for NP_001278072.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in its 5' UTR and uses a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AK134587, AL596136, BC060166, BC080274, BY133091

Consensus CDS

CCDS78985.1

UniProtKB/TrEMBL

J3QJV7

Related

ENSMUSP00000136069.2, ENSMUST00000177731.8

Conserved Domains (3) summary

pfam03528
Location:1 → 411

Rabaptin; Rabaptin

pfam09311
Location:449 → 755

Rab5-bind; Rabaptin-like protein

pfam10267
Location:564 → 700

Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein
NM_019400.3 → NP_062273.2 rab GTPase-binding effector protein 1 isoform 1

See identical proteins and their annotated locations for NP_062273.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AK134587, BC060166, BC080274, BY133091

Consensus CDS

CCDS24968.1

UniProtKB/Swiss-Prot

A1L322, O35551, Q5QNU3, Q99L08, Q9CRP3, Q9EQF9, Q9JI94

Related

ENSMUSP00000075619.7, ENSMUST00000076270.13

Conserved Domains (4) summary

pfam03528
Location:9 → 495

Rabaptin; Rabaptin

pfam09311
Location:533 → 839

Rab5-bind; Rabaptin-like protein

pfam10267
Location:648 → 784

Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein

cl14813
Location:26 → 157

GluZincin; Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins)

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_000077.7 Reference GRCm39 C57BL/6J

Range

70735553..70833931

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006533750.5 → XP_006533813.1 rab GTPase-binding effector protein 1 isoform X1

Related

ENSMUSP00000098488.5, ENSMUST00000100928.11

Conserved Domains (2) summary

pfam03528
Location:9 → 495

Rabaptin

pfam09311
Location:518 → 804

Rab5-bind; Rabaptin-like protein
XM_036156854.1 → XP_036012747.1 rab GTPase-binding effector protein 1 isoform X2

Conserved Domains (2) summary

pfam03528
Location:1 → 307

Rabaptin

pfam09311
Location:345 → 651

Rab5-bind; Rabaptin-like protein