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
  • Ras-Related Protein Rab-39A 3 4
  • Rab-39 3 4
  • RAB39 3 4
  • RAB39A 5

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 RAB GEFs exchange GTP for GDP on RABs. Gene Ontology (GO) annotations related to this gene include GTP binding and GTPase activity. An important paralog of this gene is RAB39B.

UniProtKB/Swiss-Prot Summary 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 , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RAB39A Gene

Genomics for RAB39A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RAB39A 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
GH11J107927 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.6 553 2.8 SP1 ZNF207 IKZF1 ZNF600 ATF2 ZNF223 POLR2A ZIC2 ZBTB10 REST SLC35F2 RAB39A NPAT CWF19L2 CUL5 ALKBH8 DDX10 ASS1P13 HSALNG0086974
GH11J107882 Enhancer 0.6 Ensembl ENCODE 11.3 -46.3 -46286 0.3 NRF1 CEBPB CEBPG piR-47675-018 RAB39A SLC35F2 SLN piR-57134-035
GH11J107884 Enhancer 0.3 Ensembl 11.3 -43.4 -43447 0.4 ATF2 ATF7 RAB39A SLC35F2 SLN piR-47675-018 piR-57134-035
GH11J107922 Enhancer 0.4 Ensembl 5.9 -4.7 -4748 1.8 ZNF513 SPI1 ZNF548 piR-41306-049 piR-37807 NPAT CWF19L2 ALKBH8 SLC35F2 RAB39A HSALNG0086973 SLN
GH11J107878 Enhancer 0.2 Ensembl 11.3 -49.1 -49147 0.6 RAB39A SLC35F2 SLN ELMOD1 piR-47675-018 RF00017-922
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RAB39A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RAB39A

Genomic Locations for RAB39A Gene

Latest Assembly
chr11:107,928,448-107,963,482
(GRCh38/hg38)
Size:
35,035 bases
Orientation:
Plus strand

Previous Assembly
chr11:107,799,174-107,834,208
(GRCh37/hg19 by Entrez Gene)
Size:
35,035 bases
Orientation:
Plus strand

chr11:107,799,229-107,834,208
(GRCh37/hg19 by Ensembl)
Size:
34,980 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:

Antibodies for research

  • Abcam antibodies for RAB39A
  • Boster Bio Antibodies for RAB39A

No data available for DME Specific Peptides for RAB39A Gene

Domains & Families for RAB39A Gene

Gene Families for RAB39A Gene

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

Protein Domains for RAB39A Gene

InterPro:
Blocks:
  • Transforming protein P21 RAS signature
  • GTP-binding nuclear protein Ran
  • Ras small GTPase, Ras type
  • Ras small GTPase, Rho type

Suggested Antigen Peptide Sequences for RAB39A Gene

GenScript: Design optimal peptide antigens:
  • Ras-related protein Rab-39A (RB39A_HUMAN)

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).

Phenotypes From GWAS Catalog for RAB39A Gene

Gene Ontology (GO) - Molecular Function for RAB39A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003924 GTPase activity IEA --
GO:0005515 protein binding IPI 24349490
GO:0005525 GTP binding NAS 9119394
genes like me logo Genes that share ontologies with RAB39A: view
genes like me logo Genes that share phenotypes with RAB39A: view

Animal Models for RAB39A Gene

MGI Knock Outs for RAB39A:
  • Rab39 Rab39<tm1b(KOMP)Wtsi>

miRNA for RAB39A Gene

miRTarBase miRNAs that target RAB39A

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAB39A

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
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 RAB39A gene
Compartment Confidence
cytosol 5
lysosome 4
golgi apparatus 4
plasma membrane 3
nucleus 2
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
endosome 1
mitochondrion 0

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 21873635
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane IEA --
genes like me logo Genes that share ontologies with RAB39A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RAB39A Gene

Pathways & Interactions for RAB39A Gene

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

Pathways by source for RAB39A Gene

Gene Ontology (GO) - Biological Process for RAB39A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006914 autophagy IEA --
GO:0015031 protein transport IEA --
GO:0032482 Rab protein signal transduction IEA --
GO:0090383 phagosome acidification IMP 21255211
GO:0090385 phagosome-lysosome fusion IMP 21255211
genes like me logo Genes that share ontologies with RAB39A: view

No data available for SIGNOR curated interactions for RAB39A Gene

Drugs & Compounds for RAB39A Gene

No Compound Related Data Available

Transcripts for RAB39A Gene

mRNA/cDNA for RAB39A Gene

1 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAB39A

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

No ASD Table

Relevant External Links for RAB39A Gene

GeneLoc Exon Structure for
RAB39A

Expression for RAB39A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for RAB39A Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RAB39A

SOURCE GeneReport for Unigene cluster for RAB39A Gene:

Hs.354906

Evidence on tissue expression from TISSUES for RAB39A Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with RAB39A: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 29 30
  • 96.62 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RAB39 29 30
  • 95.39 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 94 (a)
OneToMany
-- 30
  • 89 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia RAB39 29
  • 92.01 (n)
RAB39A 30
  • 55 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rab39a 29
  • 91.4 (n)
Mouse
(Mus musculus)
Mammalia Rab39 29 16 30
  • 91.4 (n)
OneToOne
Chicken
(Gallus gallus)
Aves RAB39A 30
  • 90 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RAB39A 30
  • 67 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii rab42b 30
  • 53 (a)
ManyToMany
Fruit Fly
(Drosophila melanogaster)
Insecta Rab39 30
  • 56 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea rab-39 30
  • 48 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 61 (a)
OneToMany
Species where no ortholog for RAB39A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for RAB39A: view image
Alliance of Genome Resources:
Additional Orthologs for RAB39A

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

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RAB39A Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for RAB39A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAB39A
Leiden Open Variation Database (LOVD)
RAB39A

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RAB39A Gene

Disorders for RAB39A Gene

Additional Disease Information for 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 AM (Genomics 1997) 2 3 4
  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
  3. Rab GTPases regulating phagosome maturation are differentially recruited to mycobacterial phagosomes. (PMID: 21255211) Seto S … Koide Y (Traffic (Copenhagen, Denmark) 2011) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for RAB39A Gene

Sources for RAB39A Gene