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Aliases for RAB5A Gene

Aliases for RAB5A Gene

  • RAB5A, Member RAS Oncogene Family 2 3 5
  • RAS-Associated Protein RAB5A 2 3
  • RAB5 3 4
  • Ras-Related Protein Rab-5A 3

External Ids for RAB5A Gene

Previous HGNC Symbols for RAB5A Gene

  • RAB5

Previous GeneCards Identifiers for RAB5A Gene

  • GC03P019319
  • GC03M019342
  • GC03P019838

Summaries for RAB5A Gene

GeneCards Summary for RAB5A Gene

RAB5A (RAB5A, Member RAS Oncogene Family) is a Protein Coding gene. Diseases associated with RAB5A include Motor Neuron Disease and Tuberous Sclerosis 2. Among its related pathways are Delta508-CFTR traffic / Sorting endosome formation in CF and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include GTP binding and GDP binding. An important paralog of this gene is RAB5C.

UniProtKB/Swiss-Prot for RAB5A Gene

  • The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. RAB5A is required for the fusion of plasma membranes and early endosomes (PubMed:10818110, PubMed:14617813, PubMed:16410077, PubMed:15378032). Contributes to the regulation of filopodia extension (PubMed:14978216). Required for the exosomal release of SDCBP, CD63, PDCD6IP and syndecan (PubMed:22660413). Regulates maturation of apoptotic cell-containing phagosomes, probably downstream of DYN2 and PIK3C3 (By similarity).

Gene Wiki entry for RAB5A Gene

Additional gene information for RAB5A Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RAB5A Gene

Genomics for RAB5A Gene

GeneHancer (GH) Regulatory Elements for RAB5A Gene

Promoters and enhancers for RAB5A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I019945 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.2 215 4.1 MLX DMAP1 YY1 ZNF213 E2F8 ZNF143 ZNF263 SP3 MEF2D SSRP1 EFHB RAB5A KAT2B PP2D1
GH03I020038 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 6.8 +94.9 94911 7.6 HDGF PKNOX1 ARID4B SIN3A FEZF1 ZNF2 ZBTB7B IRF4 YY1 POLR2B KAT2B EFHB RAB5A GC03M020054
GH03I019930 Enhancer 1.4 FANTOM5 Ensembl ENCODE 11.8 -15.5 -15478 1.6 HDGF PKNOX1 ARNT IRF4 ZNF766 GATA2 ARID2 FOS ATF7 RUNX3 EFHB RAB5A KAT2B GC03P019924 GC03P019936
GH03I020060 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 9.2 +114.1 114105 1.2 CEBPG RAD21 YY1 IRF9 ZNF121 NFE2 RFX1 RXRA HLF CEBPB GC03M020054 KAT2B RAB5A GC03M020070
GH03I020053 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 6.1 +109.1 109110 4.5 HDGF PKNOX1 NEUROD1 SIN3A FEZF1 IRF4 ETS1 YY1 FOS RUNX3 KAT2B RAB5A EFHB GC03M020054
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RAB5A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RAB5A gene promoter:

Genomic Locations for RAB5A Gene

Genomic Locations for RAB5A Gene
chr3:19,947,079-19,985,175
(GRCh38/hg38)
Size:
38,097 bases
Orientation:
Plus strand
chr3:19,988,571-20,026,667
(GRCh37/hg19)

Genomic View for RAB5A Gene

Genes around RAB5A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAB5A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAB5A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAB5A Gene

Proteins for RAB5A Gene

  • Protein details for RAB5A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P20339-RAB5A_HUMAN
    Recommended name:
    Ras-related protein Rab-5A
    Protein Accession:
    P20339
    Secondary Accessions:
    • B4DJA5
    • Q6FI44

    Protein attributes for RAB5A Gene

    Size:
    215 amino acids
    Molecular mass:
    23659 Da
    Quaternary structure:
    • Interacts with SGSM1 and SGSM3 (By similarity). Interacts with PIK3CB (By similarity). Interacts with GDI1; this promotes dissociation from membranes (PubMed:23815289). Interacts with EEA1 (PubMed:10491193, PubMed:20534488). Interacts with RIN1 and GAPVD1, which regulate its pathway, probably by acting as a GEF (PubMed:11703925, PubMed:16410077). Interacts with RINL. Interacts with ALS2CL, SUN2, ZFYVE20 and RUFY1 (PubMed:10818110, PubMed:11062261, PubMed:15388334, PubMed:14617813, PubMed:16034420). Interacts with RABEP1; one RABEP1 homodimer binds two RAB5A chains, but at opposite sides of the dimer (PubMed:15378032). Interacts with OCRL (PubMed:25869668). Interacts with INPP5F. May be a component of a complex composed of RAB5A, DYN2 and PIK3C3 (By similarity). Does not interact with BLOC-3 complex (heterodimer of HPS1 and HPS4) (By similarity). Interacts with CLN5 (PubMed:22431521).

    Three dimensional structures from OCA and Proteopedia for RAB5A Gene

    Alternative splice isoforms for RAB5A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RAB5A Gene

Post-translational modifications for RAB5A Gene

Other Protein References for RAB5A Gene

No data available for DME Specific Peptides for RAB5A Gene

Domains & Families for RAB5A Gene

Gene Families for RAB5A Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RAB5A Gene

Graphical View of Domain Structure for InterPro Entry

P20339

UniProtKB/Swiss-Prot:

RAB5A_HUMAN :
  • Belongs to the small GTPase superfamily. Rab family.
Family:
  • Belongs to the small GTPase superfamily. Rab family.
genes like me logo Genes that share domains with RAB5A: view

Function for RAB5A Gene

Molecular function for RAB5A Gene

GENATLAS Biochemistry:
RAB5A,Ras oncogene superfamily member,located in early endosomes
UniProtKB/Swiss-Prot EnzymeRegulation:
Regulated by guanine nucleotide exchange factors (GEFs) which promote the exchange of bound GDP for free GTP.
UniProtKB/Swiss-Prot Function:
The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. RAB5A is required for the fusion of plasma membranes and early endosomes (PubMed:10818110, PubMed:14617813, PubMed:16410077, PubMed:15378032). Contributes to the regulation of filopodia extension (PubMed:14978216). Required for the exosomal release of SDCBP, CD63, PDCD6IP and syndecan (PubMed:22660413). Regulates maturation of apoptotic cell-containing phagosomes, probably downstream of DYN2 and PIK3C3 (By similarity).

Phenotypes From GWAS Catalog for RAB5A Gene

Gene Ontology (GO) - Molecular Function for RAB5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003924 GTPase activity TAS,IDA 15378032
GO:0005515 protein binding IPI 7957092
GO:0005525 GTP binding IDA 15378032
GO:0019001 guanyl nucleotide binding IEA --
GO:0019003 GDP binding IDA 15378032
genes like me logo Genes that share ontologies with RAB5A: view
genes like me logo Genes that share phenotypes with RAB5A: view

Animal Models for RAB5A Gene

MGI Knock Outs for RAB5A:

Animal Model Products

Clone Products

  • Addgene plasmids for RAB5A

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RAB5A Gene

Localization for RAB5A Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAB5A Gene

Cell membrane; Lipid-anchor; Cytoplasmic side. Early endosome membrane; Lipid-anchor. Melanosome. Cytoplasmic vesicle. Cell projection, ruffle. Membrane. Cytoplasm, cytosol. Cytoplasmic vesicle, phagosome membrane. Endosome membrane. Note=Enriched in stage I melanosomes (PubMed:17081065). Alternates between membrane-bound and cytosolic forms (Probable). {ECO:0000269 PubMed:17081065, ECO:0000305}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RAB5A gene
Compartment Confidence
extracellular 5
cytosol 5
endosome 5
plasma membrane 4
cytoskeleton 3
mitochondrion 3
lysosome 3
endoplasmic reticulum 2
golgi apparatus 2
nucleus 1

Gene Ontology (GO) - Cellular Components for RAB5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001726 ruffle IEA --
GO:0005737 cytoplasm IDA 21266579
GO:0005768 endosome ISS --
GO:0005769 early endosome IDA,TAS 15078902
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with RAB5A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RAB5A Gene

Pathways & Interactions for RAB5A Gene

genes like me logo Genes that share pathways with RAB5A: view

SIGNOR curated interactions for RAB5A Gene

Is activated by:

Gene Ontology (GO) - Biological Process for RAB5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006661 phosphatidylinositol biosynthetic process TAS --
GO:0006810 transport IEA --
GO:0006897 endocytosis TAS,IDA 15378032
GO:0006909 phagocytosis IEA --
GO:0007596 blood coagulation TAS --
genes like me logo Genes that share ontologies with RAB5A: view

Drugs & Compounds for RAB5A Gene

(15) Drugs for RAB5A Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine diphosphate Experimental Pharma Target 0
Guanosine triphosphate Experimental Pharma Target 0
L-methionine (S)-S-oxide Experimental Pharma Target 0
Guanosine monophosphate Experimental Pharma 0

(8) Additional Compounds for RAB5A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with RAB5A: view

Transcripts for RAB5A Gene

Unigene Clusters for RAB5A Gene

RAB5A, member RAS oncogene family:
Representative Sequences:

Clone Products

  • Addgene plasmids for RAB5A

Alternative Splicing Database (ASD) splice patterns (SP) for RAB5A Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9
SP1: - - -
SP2: - -
SP3: - -
SP4: - -
SP5: - -
SP6: - - -

Relevant External Links for RAB5A Gene

GeneLoc Exon Structure for
RAB5A
ECgene alternative splicing isoforms for
RAB5A

Expression for RAB5A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RAB5A Gene

Protein differential expression in normal tissues from HIPED for RAB5A Gene

This gene is overexpressed in Nasal epithelium (8.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RAB5A Gene



Protein tissue co-expression partners for RAB5A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RAB5A Gene:

RAB5A

SOURCE GeneReport for Unigene cluster for RAB5A Gene:

Hs.475663

Evidence on tissue expression from TISSUES for RAB5A Gene

  • Nervous system(4.9)
  • Kidney(3.2)
  • Heart(2.4)
  • Skin(2.4)
  • Liver(2.2)
  • Lung(2.2)
  • Blood(2.1)
  • Spleen(2.1)
  • Intestine(2)
  • Muscle(2)
genes like me logo Genes that share expression patterns with RAB5A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RAB5A Gene

Orthologs for RAB5A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RAB5A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RAB5A 34 33
  • 99.69 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RAB5A 34
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RAB5A 33 34
  • 95.19 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RAB5A 34
  • 94 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rab5a 33
  • 91.63 (n)
cow
(Bos Taurus)
Mammalia RAB5A 33 34
  • 91.32 (n)
mouse
(Mus musculus)
Mammalia Rab5a 16 34 33
  • 91.32 (n)
chicken
(Gallus gallus)
Aves RAB5A 33 34
  • 87.91 (n)
lizard
(Anolis carolinensis)
Reptilia RAB5A 34
  • 95 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rab5a 33
  • 79.69 (n)
zebrafish
(Danio rerio)
Actinopterygii rab5ab 34
  • 92 (a)
OneToMany
rab5aa 33 34
  • 75.19 (n)
fruit fly
(Drosophila melanogaster)
Insecta Rab5 34
  • 73 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rab-5 33 34
  • 69.43 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS21 34 36
  • 53 (a)
ManyToMany
YPT53 34
  • 46 (a)
ManyToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons RHA1 33
  • 66.48 (n)
rice
(Oryza sativa)
Liliopsida Os12g0631100 33
  • 65.88 (n)
Os.14113 33
corn
(Zea mays)
Liliopsida Zm.885 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.11163 34
  • 67 (a)
OneToMany
Species where no ortholog for RAB5A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RAB5A Gene

ENSEMBL:
Gene Tree for RAB5A (if available)
TreeFam:
Gene Tree for RAB5A (if available)

Paralogs for RAB5A Gene

Pseudogenes.org Pseudogenes for RAB5A Gene

genes like me logo Genes that share paralogs with RAB5A: view

Variants for RAB5A Gene

Sequence variations from dbSNP and Humsavar for RAB5A Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000008923 -- 19,972,896(+) G/T intron_variant
rs1000059690 -- 19,953,463(+) A/G intron_variant
rs1000064398 -- 19,972,680(+) G/T intron_variant
rs1000094463 -- 19,972,674(+) A/T intron_variant
rs1000135263 -- 19,958,880(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RAB5A Gene

Variant ID Type Subtype PubMed ID
esv1338718 CNV deletion 17803354
esv23068 CNV gain+loss 19812545
esv2724999 CNV deletion 23290073
esv2725000 CNV deletion 23290073
esv2725001 CNV deletion 23290073
esv35078 CNV gain 17911159
esv3893667 CNV gain 25118596
esv996397 CNV deletion 20482838
nsv1010123 CNV gain 25217958
nsv1072676 CNV deletion 25765185
nsv1147701 CNV deletion 26484159
nsv237606 CNV deletion 16902084
nsv433358 CNV gain 18776910
nsv956838 CNV deletion 24416366
nsv997486 CNV gain 25217958

Variation tolerance for RAB5A Gene

Residual Variation Intolerance Score: 33.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.51; 11.13% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RAB5A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAB5A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAB5A Gene

Disorders for RAB5A Gene

MalaCards: The human disease database

(3) MalaCards diseases for RAB5A Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
motor neuron disease
  • motor neuron diseases
tuberous sclerosis 2
  • ts
spinocerebellar ataxia 11
  • sca11
- elite association - COSMIC cancer census association via MalaCards
Search RAB5A in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RAB5A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with RAB5A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RAB5A Gene

Publications for RAB5A Gene

  1. Direct interaction of EEA1 with Rab5b. (PMID: 10491193) Callaghan J … Stenmark H (European journal of biochemistry 1999) 3 4 22 58
  2. Sac2/INPP5F is an inositol 4-phosphatase that functions in the endocytic pathway. (PMID: 25869668) Nakatsu F … De Camilli P (The Journal of cell biology 2015) 3 4 58
  3. Rab1a and Rab5a preferentially bind to binary lipid compositions with higher stored curvature elastic energy. (PMID: 23815289) Kirsten ML … Ces O (Molecular membrane biology 2013) 3 4 58
  4. The role of ceroid lipofuscinosis neuronal protein 5 (CLN5) in endosomal sorting. (PMID: 22431521) Mamo A … Lefrancois S (Molecular and cellular biology 2012) 3 4 58
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58

Products for RAB5A Gene

Sources for RAB5A Gene

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