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Aliases for RAB5B Gene

Aliases for RAB5B Gene

  • RAB5B, Member RAS Oncogene Family 2 3 5

External Ids for RAB5B Gene

Previous GeneCards Identifiers for RAB5B Gene

  • GC12M056195
  • GC12P056944
  • GC12P056084
  • GC12P054654
  • GC12P056368
  • GC12P053407

Summaries for RAB5B Gene

GeneCards Summary for RAB5B Gene

RAB5B (RAB5B, Member RAS Oncogene Family) is a Protein Coding gene. Among its related pathways are Metabolism of proteins and Innate Immune System. 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 RAB5B Gene

  • Protein transport. Probably involved in vesicular traffic (By similarity).

Gene Wiki entry for RAB5B Gene

Additional gene information for RAB5B Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RAB5B Gene

Genomics for RAB5B Gene

GeneHancer (GH) Regulatory Elements for RAB5B Gene

Promoters and enhancers for RAB5B 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
GH12I055970 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 -1.0 -976 5.1 ZFP64 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 PMEL RAB5B BAZ2A DNAJC14 ZC3H10 ENSG00000258199 ENSG00000258317 TMEM198B CDK2 ENSG00000257740
GH12I056040 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 26 +68.1 68086 3.3 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 RPS26 LOC105369780 BAZ2A RN7SL809P STAT2 PAN2 ENSG00000258199 ZC3H10 CDK2 ENSG00000257740
GH12I055995 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 30.5 +22.8 22828 3.4 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B SUOX RAB5B DNAJC14 ZC3H10 ENSG00000258317 PRIM1 BAZ2A PMEL GC12P055992
GH12I056016 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 26 +46.5 46470 6.8 HDGF PKNOX1 ATF1 SIN3A ARID2 RXRA GTF2B REST ZNF592 MEF2D IKZF4 RAB5B BAZ2A PMEL PYM1 RN7SL809P DNAJC14 STAT2 RPS26 LOC105369781
GH12I056078 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 19.9 +107.4 107382 6.1 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC SSRP1 ZNF610 ERBB3 SUOX ANKRD52 RAB5B IKZF4 BAZ2A PHC1P1 ENSG00000257740 PAN2 SMARCC2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RAB5B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RAB5B gene promoter:

Genomic Locations for RAB5B Gene

Genomic Locations for RAB5B Gene
chr12:55,973,913-55,996,683
(GRCh38/hg38)
Size:
22,771 bases
Orientation:
Plus strand
chr12:56,367,697-56,388,490
(GRCh37/hg19)

Genomic View for RAB5B Gene

Genes around RAB5B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAB5B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAB5B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAB5B Gene

Proteins for RAB5B Gene

  • Protein details for RAB5B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P61020-RAB5B_HUMAN
    Recommended name:
    Ras-related protein Rab-5B
    Protein Accession:
    P61020
    Secondary Accessions:
    • A8K982
    • B4DKD7
    • P35239
    • P35277
    • Q6PIK9
    • Q86TH0
    • Q8IXL2

    Protein attributes for RAB5B Gene

    Size:
    215 amino acids
    Molecular mass:
    23707 Da
    Quaternary structure:
    • Binds EEA1. Interacts with RIN2 and RIN3, which probably regulate its pathway, possibly by acting as GEFs.
    SequenceCaution:
    • Sequence=AAH40143.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RAB5B Gene

    Alternative splice isoforms for RAB5B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RAB5B Gene

Post-translational modifications for RAB5B Gene

  • Ubiquitination at Lys134
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RAB5B Gene

Domains & Families for RAB5B Gene

Gene Families for RAB5B Gene

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

Suggested Antigen Peptide Sequences for RAB5B Gene

Graphical View of Domain Structure for InterPro Entry

P61020

UniProtKB/Swiss-Prot:

RAB5B_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 RAB5B: view

Function for RAB5B Gene

Molecular function for RAB5B Gene

GENATLAS Biochemistry:
RAB5B,Ras oncogene superfamily member,involved in endocytosis,expressed in skeletal muscle
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:
Protein transport. Probably involved in vesicular traffic (By similarity).

Phenotypes From GWAS Catalog for RAB5B Gene

Gene Ontology (GO) - Molecular Function for RAB5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003924 GTPase activity IEA,IDA 17562788
GO:0005515 protein binding IPI 10491193
GO:0005525 GTP binding IEA --
GO:0019003 GDP binding IDA 20937701
GO:0030742 GTP-dependent protein binding IDA 10491193
genes like me logo Genes that share ontologies with RAB5B: view
genes like me logo Genes that share phenotypes with RAB5B: view

Animal Model Products

  • Taconic Biosciences Mouse Models for RAB5B

miRNA for RAB5B Gene

miRTarBase miRNAs that target RAB5B

Clone Products

  • Addgene plasmids for RAB5B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RAB5B Gene

Localization for RAB5B Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAB5B Gene

Cell membrane; Lipid-anchor; Cytoplasmic side. Early endosome membrane; Lipid-anchor. Melanosome. Note=Enriched in stage I melanosomes.

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 RAB5B gene
Compartment Confidence
extracellular 5
endosome 5
plasma membrane 3
mitochondrion 3
cytosol 3
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RAB5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IDA --
GO:0005768 endosome IDA,IEA 10491193
GO:0005769 early endosome IBA --
GO:0005886 plasma membrane TAS,IBA --
GO:0016020 membrane TAS 1541686
genes like me logo Genes that share ontologies with RAB5B: view

Pathways & Interactions for RAB5B Gene

genes like me logo Genes that share pathways with RAB5B: view

SIGNOR curated interactions for RAB5B Gene

Other effect:

Gene Ontology (GO) - Biological Process for RAB5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0007032 endosome organization IEA --
GO:0015031 protein transport IEA --
GO:0019882 antigen processing and presentation IMP 19717423
GO:0030100 regulation of endocytosis IBA --
genes like me logo Genes that share ontologies with RAB5B: view

Drugs & Compounds for RAB5B Gene

(3) Drugs for RAB5B Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine diphosphate Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with RAB5B: view

Transcripts for RAB5B Gene

Unigene Clusters for RAB5B Gene

RAB5B, member RAS oncogene family:
Representative Sequences:

Clone Products

  • Addgene plasmids for RAB5B

Alternative Splicing Database (ASD) splice patterns (SP) for RAB5B Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b · 9c · 9d
SP1:
SP2: - - -
SP3: - -
SP4:
SP5: -
SP6:
SP7: - -

Relevant External Links for RAB5B Gene

GeneLoc Exon Structure for
RAB5B
ECgene alternative splicing isoforms for
RAB5B

Expression for RAB5B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RAB5B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RAB5B Gene

This gene is overexpressed in Nasal epithelium (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RAB5B Gene



Protein tissue co-expression partners for RAB5B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RAB5B Gene:

RAB5B

SOURCE GeneReport for Unigene cluster for RAB5B Gene:

Hs.157659

Evidence on tissue expression from TISSUES for RAB5B Gene

  • Nervous system(4.9)
  • Skin(4.7)
  • Eye(4.2)
  • Kidney(2.4)
  • Muscle(2.3)
genes like me logo Genes that share expression patterns with RAB5B: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RAB5B Gene

Orthologs for RAB5B Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RAB5B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RAB5B 33 34
  • 99.84 (n)
dog
(Canis familiaris)
Mammalia RAB5B 33 34
  • 95.35 (n)
cow
(Bos Taurus)
Mammalia RAB5B 33 34
  • 94.57 (n)
mouse
(Mus musculus)
Mammalia Rab5b 33 16 34
  • 92.87 (n)
rat
(Rattus norvegicus)
Mammalia Rab5b 33
  • 92.56 (n)
chicken
(Gallus gallus)
Aves RAB5B 33 34
  • 83.26 (n)
lizard
(Anolis carolinensis)
Reptilia RAB5B 34
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rab5b 33
  • 80.31 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.3907 33
zebrafish
(Danio rerio)
Actinopterygii rab5b 34
  • 77 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Rab5 35 34
  • 74 (a)
chrw 35
  • 41 (a)
worm
(Caenorhabditis elegans)
Secernentea rab-5 34
  • 77 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS21 33 34
  • 59.54 (n)
YPT53 34
  • 42 (a)
ManyToMany
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C13728g 33
  • 56.23 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL084C 33
  • 55.44 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.7710 33
rice
(Oryza sativa)
Liliopsida Os.11076 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.11163 34
  • 69 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU06410 33
  • 59.71 (n)
Species where no ortholog for RAB5B was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RAB5B Gene

ENSEMBL:
Gene Tree for RAB5B (if available)
TreeFam:
Gene Tree for RAB5B (if available)

Paralogs for RAB5B Gene

genes like me logo Genes that share paralogs with RAB5B: view

Variants for RAB5B Gene

Sequence variations from dbSNP and Humsavar for RAB5B Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000002373 -- 55,973,570(+) C/T upstream_transcript_variant
rs1000461817 -- 55,992,792(+) G/A 3_prime_UTR_variant
rs1000568856 -- 55,972,446(+) T/C/G upstream_transcript_variant
rs1000630792 -- 55,978,738(+) G/A intron_variant
rs1000638422 -- 55,991,646(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RAB5B Gene

Variant ID Type Subtype PubMed ID
nsv1051961 CNV gain 25217958
nsv832424 CNV loss 17160897
nsv973073 CNV duplication 23825009

Variation tolerance for RAB5B Gene

Residual Variation Intolerance Score: 60.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.09; 22.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RAB5B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAB5B

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAB5B Gene

Disorders for RAB5B Gene

Additional Disease Information for RAB5B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for RAB5B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RAB5B Gene

Publications for RAB5B Gene

  1. Identification and subcellular localization of human rab5b, a new member of the ras-related superfamily of GTPases. (PMID: 1541686) Wilson DB … Wilson MP (The Journal of clinical investigation 1992) 2 3 4 22 58
  2. Direct interaction of EEA1 with Rab5b. (PMID: 10491193) Callaghan J … Stenmark H (European journal of biochemistry 1999) 3 4 22 58
  3. Common variants in FOXP1 are associated with generalized vitiligo. (PMID: 20526340) Jin Y … Spritz RA (Nature genetics 2010) 3 44 58
  4. A novel susceptibility locus for type 1 diabetes on Chr12q13 identified by a genome-wide association study. (PMID: 18198356) Hakonarson H … Polychronakos C (Diabetes 2008) 3 44 58
  5. Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes. (PMID: 17081065) Chi A … Hunt DF (Journal of proteome research 2006) 3 4 58

Products for RAB5B Gene

  • Addgene plasmids for RAB5B

Sources for RAB5B Gene

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