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Aliases for RUBCN Gene

Aliases for RUBCN Gene

  • RUN And Cysteine Rich Domain Containing Beclin 1 Interacting Protein 2 3 5
  • KIAA0226 2 3 4
  • RUN Domain And Cysteine-Rich Domain Containing, Beclin 1-Interacting Protein 2 3
  • Beclin-1 Associated RUN Domain Containing Protein 3 4
  • RUBICON 3 4
  • Baron 3 4
  • Run Domain Beclin-1-Interacting And Cysteine-Rich Domain-Containing Protein 3
  • Rundataxin 3
  • SCAR15 3

External Ids for RUBCN Gene

Previous HGNC Symbols for RUBCN Gene

  • KIAA0226

Summaries for RUBCN Gene

Entrez Gene Summary for RUBCN Gene

  • The protein encoded by this gene is a negative regulator of autophagy and endocytic trafficking and controls endosome maturation. This protein contains two conserved domains, an N-terminal RUN domain and a C-terminal DUF4206 domain. The RUN domain is involved in Ras-like GTPase signaling, and the DUF4206 domain contains a diacylglycerol (DAG) binding-like motif. Mutation in this gene results in deletion of the DAG binding-like motif and causes a recessive ataxia. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Apr 2014]

GeneCards Summary for RUBCN Gene

RUBCN (RUN And Cysteine Rich Domain Containing Beclin 1 Interacting Protein) is a Protein Coding gene. Diseases associated with RUBCN include Spinocerebellar Ataxia, Autosomal Recessive 15 and Alacrima, Achalasia, And Mental Retardation Syndrome. Among its related pathways are Autophagy - animal and Apoptosis and Autophagy. An important paralog of this gene is RUBCNL.

UniProtKB/Swiss-Prot for RUBCN Gene

  • Inhibits PIK3C3 activity; under basal conditions negatively regulates PI3K complex II (PI3KC3-C2) function in autophagy. Negatively regulates endosome maturation and degradative endocytic trafficking and impairs autophagosome maturation process. Can sequester UVRAG from association with a class C Vps complex (possibly the HOPS complex) and negatively regulates Rab7 activation (PubMed:20974968, PubMed:21062745).

  • Involved in regulation of pathogen-specific host defense of activated macrophages. Following bacterial infection promotes NADH oxidase activity by association with CYBA thereby affecting TLR2 signaling and probably other TLR-NOX pathways. Stabilizes the CYBA:CYBB NADPH oxidase heterodimer, increases its association with TLR2 and its phagosome trafficking to induce antimicrobial burst of ROS and production of inflammatory cytokines (PubMed:22423966). Following fungal or viral infection (implicating CLEC7A (dectin-1)-mediated myeloid cell activation or DDX58/RIG-I-dependent sensing of RNA viruses) negatively regulates pro-inflammatory cytokine production by association with CARD9 and sequestering it from signaling complexes (PubMed:22423967).

Additional gene information for RUBCN Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RUBCN Gene

Genomics for RUBCN Gene

GeneHancer (GH) Regulatory Elements for RUBCN Gene

Promoters and enhancers for RUBCN 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
GH03I197748 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 555.7 -0.6 -612 4.3 HDGF PKNOX1 ARNT SIN3A YBX1 ZNF2 ZBTB7B YY1 POLR2B ZNF766 RUBCN FYTTD1 LRCH3 ENSG00000249626 IQCG GC03P197788
GH03I197733 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 552.3 +13.9 13940 5 HDGF PKNOX1 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 RUBCN FYTTD1 LOC220729 IQCG LRCH3 PIR54031
GH03I197820 Enhancer 0.9 ENCODE 10.6 -71.3 -71303 1.6 FOXA2 MLX ARID4B DMAP1 ZNF48 ZSCAN9 RAD21 RARA YY1 THAP11 LRCH3 RUBCN FYTTD1 MIR922 LOC220729 ENSG00000234136
GH03I197807 Enhancer 0.8 Ensembl ENCODE 10.7 -60.3 -60260 4.9 ZNF362 ZNF571 HLF ZNF384 ATF2 ZFP69B ZNF324 ZFHX2 ZNF692 ZNF629 ENSG00000234136 SENP5 RUBCN FYTTD1 LMLN MELTF-AS1 LRCH3
GH03I197879 Enhancer 0.8 ENCODE 10.5 -130.9 -130879 1.2 ELF3 FOXA2 MLX RARA CREM MIXL1 HMG20B SP5 PPARG NFIL3 RUBCN FYTTD1 IQCG SEPT14P3 GC03P197886 LOC105374310 LRCH3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RUBCN on UCSC Golden Path with GeneCards custom track

Genomic Locations for RUBCN Gene

Genomic Locations for RUBCN Gene
chr3:197,671,393-197,749,727
(GRCh38/hg38)
Size:
78,335 bases
Orientation:
Minus strand
chr3:197,398,259-197,476,598
(GRCh37/hg19)

Genomic View for RUBCN Gene

Genes around RUBCN on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for RUBCN Gene

Proteins for RUBCN Gene

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

    Protein Symbol:
    Q92622-RUBIC_HUMAN
    Recommended name:
    Run domain Beclin-1-interacting and cysteine-rich domain-containing protein
    Protein Accession:
    Q92622
    Secondary Accessions:
    • Q96CK5

    Protein attributes for RUBCN Gene

    Size:
    972 amino acids
    Molecular mass:
    108622 Da
    Quaternary structure:
    • Associates with PI3K (PI3KC3/PI3K-III/class III phosphatidylinositol 3-kinase) complex II (PI3KC3-C2) in which the core composed of the catalytic subunit PIK3C3, the regulatory subunit PIK3R4 and BECN1 is associated with UVRAG; in the complex interacts directly with PI3KC3 and UVRAG (PubMed:19270696, PubMed:21062745). Interacts with Rab7 (RAB7A or RAB7B) (GTP-bound form); Rab7 and UVRAG compete for RUBCN binding; can interact simultaneously with Rab7 and the PI3K complex (PubMed:20943950, PubMed:20974968, PubMed:21062745). Interacts with CYBA and CYBB; indicative for the association with the CYBA:CYBB NADPH oxidase heterodimer. Interacts with NOX4 and probably associates with the CYBA:NOX4 complex (PubMed:22423966). Interacts with YWHAB and CARD9 in a competetive and stimulation-dependent manner; RUBCN exchanges interaction from YWHAB to CARD9 upon stimulation with beta-1,3-glucan (PubMed:22423967).
    SequenceCaution:
    • Sequence=BAA13215.3; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for RUBCN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RUBCN Gene

Post-translational modifications for RUBCN Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RUBCN Gene

Domains & Families for RUBCN Gene

Gene Families for RUBCN Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for RUBCN Gene

Suggested Antigen Peptide Sequences for RUBCN Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RUBCN: view

No data available for UniProtKB/Swiss-Prot for RUBCN Gene

Function for RUBCN Gene

Molecular function for RUBCN Gene

UniProtKB/Swiss-Prot Function:
Inhibits PIK3C3 activity; under basal conditions negatively regulates PI3K complex II (PI3KC3-C2) function in autophagy. Negatively regulates endosome maturation and degradative endocytic trafficking and impairs autophagosome maturation process. Can sequester UVRAG from association with a class C Vps complex (possibly the HOPS complex) and negatively regulates Rab7 activation (PubMed:20974968, PubMed:21062745).
UniProtKB/Swiss-Prot Function:
Involved in regulation of pathogen-specific host defense of activated macrophages. Following bacterial infection promotes NADH oxidase activity by association with CYBA thereby affecting TLR2 signaling and probably other TLR-NOX pathways. Stabilizes the CYBA:CYBB NADPH oxidase heterodimer, increases its association with TLR2 and its phagosome trafficking to induce antimicrobial burst of ROS and production of inflammatory cytokines (PubMed:22423966). Following fungal or viral infection (implicating CLEC7A (dectin-1)-mediated myeloid cell activation or DDX58/RIG-I-dependent sensing of RNA viruses) negatively regulates pro-inflammatory cytokine production by association with CARD9 and sequestering it from signaling complexes (PubMed:22423967).

Gene Ontology (GO) - Molecular Function for RUBCN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19270696
genes like me logo Genes that share ontologies with RUBCN: view
genes like me logo Genes that share phenotypes with RUBCN: view

Human Phenotype Ontology for RUBCN Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for RUBCN Gene

Localization for RUBCN Gene

Subcellular locations from UniProtKB/Swiss-Prot for RUBCN Gene

Late endosome. Lysosome. Early endosome. Note=Predominantly located in late endosomes/lysosomes, only partially detected in early endosome and not at all in the Golgi apparatus.

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 RUBCN gene
Compartment Confidence
nucleus 5
cytosol 5
endosome 5
lysosome 4

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RUBCN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005764 lysosome IEA --
GO:0005768 endosome IEA --
GO:0005769 early endosome IDA,IEA 19270696
GO:0005770 late endosome IDA,IEA 19270696
genes like me logo Genes that share ontologies with RUBCN: view

Pathways & Interactions for RUBCN Gene

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

Pathways by source for RUBCN Gene

1 KEGG pathway for RUBCN Gene
1 Cell Signaling Technology pathway for RUBCN Gene

SIGNOR curated interactions for RUBCN Gene

Inactivates:

Gene Ontology (GO) - Biological Process for RUBCN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002376 immune system process IEA --
GO:0006897 endocytosis IEA --
GO:0006909 phagocytosis IEA --
GO:0006914 autophagy IEA --
GO:0010507 negative regulation of autophagy IMP 19270696
genes like me logo Genes that share ontologies with RUBCN: view

Drugs & Compounds for RUBCN Gene

No Compound Related Data Available

Transcripts for RUBCN Gene

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for RUBCN Gene

GeneLoc Exon Structure for
RUBCN
ECgene alternative splicing isoforms for
RUBCN

Expression for RUBCN Gene

NURSA nuclear receptor signaling pathways regulating expression of RUBCN Gene:

RUBCN

Evidence on tissue expression from TISSUES for RUBCN Gene

  • Kidney(4.2)
  • Bone marrow(4.1)
  • Nervous system(3.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RUBCN Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • eye
  • head
Limb:
  • lower limb
General:
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with RUBCN: view

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for RUBCN Gene

Orthologs for RUBCN Gene

This gene was present in the common ancestor of animals.

Orthologs for RUBCN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ptr-mir-922 34
  • 99 (a)
OneToOne
KIAA0226 33
  • 98.92 (n)
dog
(Canis familiaris)
Mammalia KIAA0226 33 34
  • 90.91 (n)
cow
(Bos Taurus)
Mammalia KIAA0226 33 34
  • 90.17 (n)
mouse
(Mus musculus)
Mammalia 1700021K19Rik 33 34
  • 86.31 (n)
Rubcn 16
rat
(Rattus norvegicus)
Mammalia RGD1305422 33
  • 85.9 (n)
oppossum
(Monodelphis domestica)
Mammalia KIAA0226 34
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KIAA0226 34
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves KIAA0226 33 34
  • 74.68 (n)
lizard
(Anolis carolinensis)
Reptilia KIAA0226 34
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kiaa0226 33
  • 64.48 (n)
zebrafish
(Danio rerio)
Actinopterygii si:ch1073-280h16.1 33 34
  • 61.61 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG12772 34
  • 30 (a)
OneToOne
Species where no ortholog for RUBCN 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for RUBCN Gene

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

Paralogs for RUBCN Gene

Paralogs for RUBCN Gene

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

Variants for RUBCN Gene

Sequence variations from dbSNP and Humsavar for RUBCN Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs587777235 pathogenic, Spinocerebellar ataxia, autosomal recessive 15 197,676,907(-) G/ coding_sequence_variant, frameshift
rs767982852 pathogenic, Cerebral hypomyelination, Elbow flexion contracture, Global developmental delay, Intellectual disability, Knee flexion contracture, Muscular hypotonia, Nystagmus 197,694,417(-) T/C coding_sequence_variant, missense_variant
rs28394098 likely-benign, not specified 197,700,686(-) A/C/G coding_sequence_variant, synonymous_variant
rs28562770 likely-benign, not specified 197,675,081(-) T/C coding_sequence_variant, synonymous_variant
rs60457064 likely-benign, not specified 197,705,158(-) C/A/T 5_prime_UTR_variant, coding_sequence_variant, synonymous_variant

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

Variant ID Type Subtype PubMed ID
dgv2904e59 CNV duplication 20981092
dgv5042n100 CNV gain 25217958
esv1514481 CNV insertion 17803354
esv25937 CNV loss 19812545
esv2663109 CNV deletion 23128226
esv2668997 CNV deletion 23128226
esv2726672 CNV deletion 23290073
esv2726674 CNV deletion 23290073
esv2751989 CNV gain 17911159
esv2759214 CNV gain+loss 17122850
esv2763718 CNV gain+loss 21179565
esv3569233 CNV loss 25503493
esv3569234 CNV loss 25503493
esv3575646 CNV gain 25503493
esv3599313 CNV gain 21293372
esv3599318 CNV gain 21293372
esv3599319 CNV gain 21293372
esv3599320 CNV loss 21293372
esv3599321 CNV loss 21293372
esv3599322 CNV gain 21293372
esv995678 CNV insertion 20482838
nsv1011831 CNV gain 25217958
nsv10402 CNV gain 18304495
nsv1115652 CNV duplication 24896259
nsv1128880 CNV duplication 24896259
nsv1146717 CNV duplication 26484159
nsv1151147 CNV insertion 26484159
nsv236569 CNV insertion 16902084
nsv428433 CNV gain+loss 18775914
nsv508983 CNV insertion 20534489
nsv829831 CNV loss 17160897
nsv829832 CNV loss 17160897

Variation tolerance for RUBCN Gene

Residual Variation Intolerance Score: 41.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.23; 81.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RUBCN Gene

Human Gene Mutation Database (HGMD)
RUBCN
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RUBCN

SNP Genotyping and Copy Number Assay Products

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

Disorders for RUBCN Gene

MalaCards: The human disease database

(3) MalaCards diseases for RUBCN Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search RUBCN in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RUBIC_HUMAN
  • Spinocerebellar ataxia, autosomal recessive, 15 (SCAR15) [MIM:615705]: Spinocerebellar ataxia defines a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAR15 patients manifest cerebellar ataxia in early childhood and delayed motor development with delayed walking. Additional features include dysarthria, upper limb involvement, abnormal eye movements, and hyporeflexia. {ECO:0000269 PubMed:20826435}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with RUBCN: view

No data available for Genatlas for RUBCN Gene

Publications for RUBCN Gene

  1. Rundataxin, a novel protein with RUN and diacylglycerol binding domains, is mutant in a new recessive ataxia. (PMID: 20826435) Assoum M … Koenig M (Brain : a journal of neurology 2010) 2 3 4 58
  2. Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. (PMID: 9039502) Nagase T … Nomura N (DNA research : an international journal for rapid publication of reports on genes and genomes 1996) 2 3 4 58
  3. Autophagy protein Rubicon mediates phagocytic NADPH oxidase activation in response to microbial infection or TLR stimulation. (PMID: 22423966) Yang CS … Jung JU (Cell host & microbe 2012) 3 4 58
  4. The autophagy regulator Rubicon is a feedback inhibitor of CARD9-mediated host innate immunity. (PMID: 22423967) Yang CS … Jung JU (Cell host & microbe 2012) 3 4 58
  5. The RUN domain of rubicon is important for hVps34 binding, lipid kinase inhibition, and autophagy suppression. (PMID: 21062745) Sun Q … Zhong Q (The Journal of biological chemistry 2011) 3 4 58

Products for RUBCN Gene

  • Addgene plasmids for RUBCN

Sources for RUBCN Gene

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