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Aliases for RAB39A Gene

Aliases for RAB39A Gene

  • RAB39A, Member RAS Oncogene Family 2 3 5
  • RAB39, Member RAS Oncogene Family 2 3
  • Rab-Related GTP-Binding Protein 2 3
  • Rab-39 3 4
  • RAB39 3 4
  • Ras-Related Protein Rab-39A 3

External Ids for RAB39A Gene

Previous HGNC Symbols for RAB39A Gene

  • RAB39

Previous GeneCards Identifiers for RAB39A Gene

  • GC11P107799

Summaries for RAB39A Gene

GeneCards Summary for RAB39A Gene

RAB39A (RAB39A, Member RAS Oncogene Family) is a Protein Coding gene. Among its related pathways are Vesicle-mediated transport and Intra-Golgi traffic. GO annotations related to this gene include GTP binding and GTPase activity. An important paralog of this gene is RAB39B.

UniProtKB/Swiss-Prot for RAB39A Gene

  • Plays a role in the maturation and acidification of phagosomes that engulf pathogens, such as S.aureus and M.tuberculosis. Plays a role in vesicular trafficking. Plays a role in the fusion of phagosomes with lysosomes. Negatively regulates LPS-induced autophagosome formation in macrophages possibly by implicating PI3K (PubMed:24349490). May be involved in multiple neurite formation (By similarity).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RAB39A Gene

Genomics for RAB39A Gene

Regulatory Elements for RAB39A Gene

Enhancers for RAB39A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11F107882 0.2 ENCODE 11.3 -46.2 -46226 0.2 GATA3 NRF1 CEBPB ATF2 RAB39A SLC35F2 SLN RPLP2P3 LOC203930
GH11F107927 0.5 ENCODE 0.8 +0.1 109 2.0 ATF1 PKNOX1 SIN3A ZNF2 ZNF121 GLIS2 ZNF143 KLF7 FOS CEBPZ CUL5 DDX10 SLC35F2 ASS1P13 RAB39A
GH11F107929 0.6 ENCODE 0.8 +1.5 1481 0.2 ZNF133 JUNB MAFK RELA RAB39A CUL5
GH11F107948 0.6 ENCODE 0.3 +20.0 20027 0.8 SMARCA4 POLR2A ZMYM3 ACAT1 RAB39A CUL5
GH11F107957 1.2 FANTOM5 Ensembl 0.3 +28.9 28942 0.8 OSR2 SMARCA4 POLR2A IKZF1 JUNB FOXP2 REST RAD21 SLN ELMOD1 RAB39A CUL5
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around RAB39A on UCSC Golden Path with GeneCards custom track

Promoters for RAB39A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001052948 325 2001 ATF1 PKNOX1 SIN3A ZNF2 ZNF121 GLIS2 ZNF143 KLF7 FOS CEBPZ

Genomic Location for RAB39A Gene

Chromosome:
11
Start:
107,928,475 bp from pter
End:
107,963,482 bp from pter
Size:
35,008 bases
Orientation:
Plus strand

Genomic View for RAB39A Gene

Genes around RAB39A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAB39A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAB39A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAB39A Gene

Proteins for RAB39A Gene

  • Protein details for RAB39A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q14964-RB39A_HUMAN
    Recommended name:
    Ras-related protein Rab-39A
    Protein Accession:
    Q14964
    Secondary Accessions:
    • A8KAA4
    • Q8N6W2

    Protein attributes for RAB39A Gene

    Size:
    217 amino acids
    Molecular mass:
    25007 Da
    Quaternary structure:
    • Interacts with BECN1. Probably associates with the PI3K (PI3KC3/PI3K-III/class III phosphatidylinositol 3-kinase) complex (PubMed:24349490). Interacts with UACA (By similarity).

neXtProt entry for RAB39A Gene

Post-translational modifications for RAB39A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RAB39A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RAB39A Gene

Domains & Families for RAB39A Gene

Gene Families for RAB39A Gene

Suggested Antigen Peptide Sequences for RAB39A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q14964

UniProtKB/Swiss-Prot:

RB39A_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 RAB39A: view

Function for RAB39A Gene

Molecular function for RAB39A Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the maturation and acidification of phagosomes that engulf pathogens, such as S.aureus and M.tuberculosis. Plays a role in vesicular trafficking. Plays a role in the fusion of phagosomes with lysosomes. Negatively regulates LPS-induced autophagosome formation in macrophages possibly by implicating PI3K (PubMed:24349490). May be involved in multiple neurite formation (By similarity).

Gene Ontology (GO) - Molecular Function for RAB39A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0005515 protein binding IPI 24349490
GO:0005525 GTP binding NAS 9119394
genes like me logo Genes that share ontologies with RAB39A: view

Phenotypes for RAB39A Gene

MGI mutant phenotypes for RAB39A:
inferred from 1 alleles
GenomeRNAi human phenotypes for RAB39A:
genes like me logo Genes that share phenotypes with RAB39A: view

Animal Models for RAB39A Gene

MGI Knock Outs for RAB39A:

Animal Model Products

miRNA for RAB39A Gene

miRTarBase miRNAs that target RAB39A

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RAB39A Gene

Localization for RAB39A Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAB39A Gene

Cell membrane; Lipid-anchor; Cytoplasmic side. Cytoplasmic vesicle, phagosome. Cytoplasmic vesicle, phagosome membrane; Lipid-anchor; Cytoplasmic side. Lysosome. Note=Recruited to phagosomes containing S.aureus or M.tuberculosis.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RAB39A Gene COMPARTMENTS Subcellular localization image for RAB39A gene
Compartment Confidence
golgi apparatus 4
cytosol 3
lysosome 3
plasma membrane 3
vacuole 3
nucleus 2
endoplasmic reticulum 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for RAB39A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005764 lysosome IEA --
GO:0005794 Golgi apparatus IBA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with RAB39A: view

Pathways & Interactions for RAB39A Gene

genes like me logo Genes that share pathways with RAB39A: view

Gene Ontology (GO) - Biological Process for RAB39A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006914 autophagy IEA --
GO:0007264 small GTPase mediated signal transduction IEA --
GO:0015031 protein transport IEA --
GO:0090383 phagosome acidification IMP 21255211
genes like me logo Genes that share ontologies with RAB39A: view

No data available for SIGNOR curated interactions for RAB39A Gene

Transcripts for RAB39A Gene

mRNA/cDNA for RAB39A Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(6) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RAB39A Gene

RAB39A, member RAS oncogene family:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for RAB39A Gene

No ASD Table

Relevant External Links for RAB39A Gene

GeneLoc Exon Structure for
RAB39A
ECgene alternative splicing isoforms for
RAB39A

Expression for RAB39A Gene

mRNA expression in normal human tissues for RAB39A Gene

mRNA differential expression in normal tissues according to GTEx for RAB39A Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x4.2).

Protein differential expression in normal tissues from HIPED for RAB39A Gene

This gene is overexpressed in Frontal cortex (20.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RAB39A Gene



NURSA nuclear receptor signaling pathways regulating expression of RAB39A Gene:

RAB39A

SOURCE GeneReport for Unigene cluster for RAB39A Gene:

Hs.354906
genes like me logo Genes that share expression patterns with RAB39A: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for RAB39A Gene

Orthologs for RAB39A Gene

This gene was present in the common ancestor of animals.

Orthologs for RAB39A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RAB39A 34 35
  • 96.62 (n)
cow
(Bos Taurus)
Mammalia RAB39 34 35
  • 95.39 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 94 (a)
OneToMany
-- 35
  • 89 (a)
OneToMany
dog
(Canis familiaris)
Mammalia RAB39 34
  • 92.01 (n)
RAB39A 35
  • 55 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rab39 34 16 35
  • 91.4 (n)
rat
(Rattus norvegicus)
Mammalia Rab39a 34
  • 91.4 (n)
chicken
(Gallus gallus)
Aves RAB39A 35
  • 90 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RAB39A 35
  • 67 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii rab42b 35
  • 53 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta Rab39 35
  • 56 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rab-39 35
  • 48 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 61 (a)
OneToMany
Species where no ortholog for RAB39A 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for RAB39A Gene

ENSEMBL:
Gene Tree for RAB39A (if available)
TreeFam:
Gene Tree for RAB39A (if available)

Paralogs for RAB39A Gene

Pseudogenes.org Pseudogenes for RAB39A Gene

genes like me logo Genes that share paralogs with RAB39A: view

Variants for RAB39A Gene

Sequence variations from dbSNP and Humsavar for RAB39A Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1027733 -- 107,963,299(+) ctcct(C/G)gcctc utr-variant-3-prime
rs1027734 -- 107,963,381(+) CAGCA(A/C)ATGTT utr-variant-3-prime
rs10400244 -- 107,940,297(+) tcaca(G/T)tctgt intron-variant
rs10400262 -- 107,938,116(+) ccagc(A/C)ctttg intron-variant
rs10466521 -- 107,934,974(+) CTCTC(C/T)CTTCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RAB39A Gene

Variant ID Type Subtype PubMed ID
dgv1274n100 CNV gain 25217958
dgv1276n100 CNV gain 25217958
esv2750980 CNV gain 17911159
esv3579902 CNV loss 25503493
esv3579903 CNV loss 25503493
esv3627655 CNV gain 21293372
esv3627667 CNV gain 21293372
esv3627669 CNV loss 21293372
esv3627670 CNV gain 21293372
nsv1040345 CNV gain 25217958
nsv1043139 CNV gain 25217958
nsv479 CNV insertion 18451855
nsv521771 CNV gain 19592680

Variation tolerance for RAB39A Gene

Residual Variation Intolerance Score: 26.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.38; 8.33% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RAB39A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAB39A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAB39A Gene

Disorders for RAB39A Gene

Relevant External Links for RAB39A

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RAB39A

No disorders were found for RAB39A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RAB39A Gene

Publications for RAB39A Gene

  1. Construction of a transcription map around the gene for ataxia telangiectasia; identification of at least four novel genes. (PMID: 9119394) Stankovic T. … Taylor A.M.R. (Genomics 1997) 2 3 4 64
  2. Rab39a interacts with phosphatidylinositol 3-kinase and negatively regulates autophagy induced by lipopolysaccharide stimulation in macrophages. (PMID: 24349490) Seto S. … Koide Y. (PLoS ONE 2013) 3 4 64
  3. Rab GTPases regulating phagosome maturation are differentially recruited to mycobacterial phagosomes. (PMID: 21255211) Seto S. … Koide Y. (Traffic 2011) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. The late endocytic Rab39a GTPase regulates the interaction between multivesicular bodies and chlamydial inclusions. (PMID: 26163492) Gambarte Tudela J. … Damiani M.T. (J. Cell. Sci. 2015) 3 64

Products for RAB39A Gene

Sources for RAB39A Gene

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