RAB5A RAB5A, member RAS oncogene family [Homo sapiens (human)] - Gene

Summary

Official Symbol: RAB5Aprovided by HGNC
Official Full Name: RAB5A, member RAS oncogene familyprovided by HGNC
Primary source: HGNC:HGNC:9783
See related: Ensembl:ENSG00000144566 MIM:179512; AllianceGenome:HGNC:9783
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RAB5
Summary: Enables GDP binding activity; GTP binding activity; and GTPase activity. Involved in several processes, including amyloid-beta clearance by transcytosis; early endosome to late endosome transport; and regulation of exocytosis. Located in several cellular components, including cytoplasmic side of early endosome membrane; nucleoplasm; and terminal bouton. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in brain (RPKM 22.0), thyroid (RPKM 19.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p24.3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (19947097..19985175)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (19951230..19989247)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (19988589..20026667)

Chromosome 3 - NC_000003.12 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Tumor-derived hypoxic small extracellular vesicles promote endothelial cell migration and tube formation via ALS2/Rab5/beta-catenin signaling.
Title: Tumor-derived hypoxic small extracellular vesicles promote endothelial cell migration and tube formation via ALS2/Rab5/β-catenin signaling.
RAB5A in triple-negative breast cancer: a critical role in macrophage reshaping in an exosomal miR-21-dependent manner.
Title: RAB5A in triple-negative breast cancer: a critical role in macrophage reshaping in an exosomal miR-21-dependent manner.
Ras-Related Protein Rab5a Regulates Complement C5a Receptor Trafficking, Chemotaxis, and Chemokine Secretion in Human Macrophages.
Title: Ras-Related Protein Rab5a Regulates Complement C5a Receptor Trafficking, Chemotaxis, and Chemokine Secretion in Human Macrophages.
miR-451a suppresses the proliferation and migration of high-grade serous ovarian cancer by targeting RAB5A through the Ras/Raf/MEK/ERK pathway.
Title: miR-451a suppresses the proliferation and migration of high-grade serous ovarian cancer by targeting RAB5A through the Ras/Raf/MEK/ERK pathway.
A genome-wide CRISPR/Cas9 screen identifies a role for Rab5A and early endosomes in hepatitis E virus replication.
Title: A genome-wide CRISPR/Cas9 screen identifies a role for Rab5A and early endosomes in hepatitis E virus replication.
HPIP and RUFY3 are noncanonical guanine nucleotide exchange factors of Rab5 to regulate endocytosis-coupled focal adhesion turnover.
Title: HPIP and RUFY3 are noncanonical guanine nucleotide exchange factors of Rab5 to regulate endocytosis-coupled focal adhesion turnover.
Hepatitis B virus promotes its own replication by enhancing RAB5A-mediated dual activation of endosomal and autophagic vesicle pathways.
Title: Hepatitis B virus promotes its own replication by enhancing RAB5A-mediated dual activation of endosomal and autophagic vesicle pathways.
Receptor-mediated internalization promotes increased endosome size and number in a RAB4- and RAB5-dependent manner.
Title: Receptor-mediated internalization promotes increased endosome size and number in a RAB4- and RAB5-dependent manner.
RNA demethylase ALKBH5 promotes colorectal cancer progression by posttranscriptional activation of RAB5A in an m6A-YTHDF2-dependent manner.
Title: RNA demethylase ALKBH5 promotes colorectal cancer progression by posttranscriptional activation of RAB5A in an m6A-YTHDF2-dependent manner.
Identification of Key Genes and miRNAs Affecting Osteosarcoma Based on Bioinformatics.
Title: Identification of Key Genes and miRNAs Affecting Osteosarcoma Based on Bioinformatics.

Submit: New GeneRIF Correction See all GeneRIFs (160)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	HIV-1 Nef-HLA-A (MHCI) interaction localizes with RAB5A-positive early endosomes	PubMed
	nef	Interaction of HIV-1 Nef with PACS-1 occurs in cellular endosomes with markers RAB5 and LAMP-1	PubMed
	nef	Genome-wide shRNA screening identifies RAB5A, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells	PubMed
	nef	Nef-triggered MHCII endocytosis requires Rab5 activity and lyst function, whereas lysosomal trafficking of internalized MHCII molecules requires Rab7 activity	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

HSC13E052 (e-PCR)
- UniSTS:17465

RAB5A_779 (e-PCR)
- UniSTS:277647

D3S2948E (e-PCR)
- UniSTS:150932

RH91784 (e-PCR)
- UniSTS:86468

D3S3483E (e-PCR)
- UniSTS:154072

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables G protein activity	IEA Inferred from Electronic Annotation more info
enables GDP binding	IDA Inferred from Direct Assay more info	PubMed
enables GTP binding	IDA Inferred from Direct Assay more info	PubMed
enables GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
enables GTPase activity	IDA Inferred from Direct Assay more info	PubMed
enables membrane scission GTPase motor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in amyloid-beta clearance by transcytosis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in canonical Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in early endosome to late endosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in endocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in modulation by host of viral process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in phagocytosis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in receptor internalization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of autophagosome assembly	TAS Traceable Author Statement more info	PubMed
involved_in regulation of endosome size	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of filopodium assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of long-term neuronal synaptic plasticity	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of synaptic vesicle exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synaptic vesicle recycling	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in actin cytoskeleton	IEA Inferred from Electronic Annotation more info
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	ISS Inferred from Sequence or Structural Similarity more info
located_in axon terminus	ISS Inferred from Sequence or Structural Similarity more info
located_in clathrin-coated endocytic vesicle membrane	TAS Traceable Author Statement more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic side of early endosome membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
is_active_in dendrite	IBA Inferred from Biological aspect of Ancestor more info
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome membrane	TAS Traceable Author Statement more info
located_in early phagosome	ISS Inferred from Sequence or Structural Similarity more info
is_active_in endocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
is_active_in endomembrane system	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in melanosome	IEA Inferred from Electronic Annotation more info
located_in membrane raft	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in phagocytic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in phagocytic vesicle membrane	IEA Inferred from Electronic Annotation more info
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 postsynaptic early endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in ruffle	IEA Inferred from Electronic Annotation more info
located_in somatodendritic compartment	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle	ISS Inferred from Sequence or Structural Similarity more info
is_active_in synaptic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in terminal bouton	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ras-related protein Rab-5A

Names: RAS-associated protein RAB5A

NP_001278977.1

EC 3.6.5.2

NP_004153.2

EC 3.6.5.2

XP_047304604.1

EC 3.6.5.2

XP_054203388.1

EC 3.6.5.2

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_001292048.2 → NP_001278977.1 ras-related protein Rab-5A isoform 2

See identical proteins and their annotated locations for NP_001278977.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1.

Source sequence(s)

AK295992, BC018288, DA972638, DC330362

Consensus CDS

CCDS77710.1

UniProtKB/TrEMBL

A0A0A1HAN9

Related

ENSP00000411941.1, ENST00000422242.1

Conserved Domains (2) summary

cd01860
Location:20 → 168

Rab5_related; Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion

pfam00071
Location:22 → 169

Ras; Ras family
NM_004162.5 → NP_004153.2 ras-related protein Rab-5A isoform 1

See identical proteins and their annotated locations for NP_004153.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).

Source sequence(s)

AK309287, AK312618, BC018288, BJ991078, DC330362

Consensus CDS

CCDS2633.1

UniProtKB/Swiss-Prot

B4DJA5, P20339, Q6FI44

UniProtKB/TrEMBL

A0A0A1HAN9

Related

ENSP00000273047.4, ENST00000273047.9

Conserved Domains (1) summary

cd01860
Location:20 → 182

Rab5_related; Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion