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    RUBCN rubicon autophagy regulator [ Homo sapiens (human) ]

    Gene ID: 9711, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RUBCNprovided by HGNC
    Official Full Name
    rubicon autophagy regulatorprovided by HGNC
    Primary source
    HGNC:HGNC:28991
    See related
    Ensembl:ENSG00000145016 MIM:613516; AllianceGenome:HGNC:28991
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SCAR15; RUBICON; KIAA0226
    Summary
    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]
    Expression
    Ubiquitous expression in testis (RPKM 7.0), brain (RPKM 6.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RUBCN in Genome Data Viewer
    Location:
    3q29
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (197668867..197749820, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (200401254..200482196, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (197395738..197476691, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene keratinocyte proline-rich protein Neighboring gene uncharacterized LOC124909481 Neighboring gene PPP4R2 pseudogene 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:197380592-197381265 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15089 Neighboring gene MPRA-validated peak4995 silencer Neighboring gene uncharacterized LOC124906331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:197390351-197390864 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:197392407-197392920 Neighboring gene microRNA 922 Neighboring gene MPRA-validated peak4996 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21112 Neighboring gene Sharpr-MPRA regulatory region 8415 Neighboring gene Sharpr-MPRA regulatory region 6653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21114 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:197463053-197463900 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:197466398-197466530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21115 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15092 Neighboring gene forty-two-three domain containing 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:197504526-197504699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21116 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:197517785-197518499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21120 Neighboring gene leucine rich repeats and calponin homology domain containing 3 Neighboring gene uncharacterized LOC124909482 Neighboring gene uncharacterized LOC105374310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21121 Neighboring gene ribosomal protein L17 pseudogene 18

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Rundataxin, a novel protein with RUN and diacylglycerol binding domains, is mutant in a new recessive ataxia. Assoum M, et al. Brain, 2010 Aug. PMID 20826435
    2. Rubicon: LC3-associated phagocytosis and beyond. Wong SW, et al. FEBS J, 2018 Apr. PMID 29215797, Free PMC Article
    3. Hepatitis C virus enhances Rubicon expression, leading to autophagy inhibition and intracellular innate immune activation. Shiode Y, et al. Sci Rep, 2020 Sep 17. PMID 32943718, Free PMC Article
    4. Binding Rubicon to cross the Rubicon. Matsunaga K, et al. Autophagy, 2009 Aug. PMID 19550146
    5. The Salih ataxia mutation impairs Rubicon endosomal localization. Assoum M, et al. Cerebellum, 2013 Dec. PMID 23728897

    See all (64) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A RAB7A phosphoswitch coordinates Rubicon Homology protein regulation of Parkin-dependent mitophagy.
      Title: A RAB7A phosphoswitch coordinates Rubicon Homology protein regulation of Parkin-dependent mitophagy.
    2. Neuronal Rubicon Represses Extracellular APP/Amyloid beta Deposition in Alzheimer's Disease.
      Title: Neuronal Rubicon Represses Extracellular APP/Amyloid β Deposition in Alzheimer's Disease.
    3. Epigenome-wide three-way interaction study identifies a complex pattern between TRIM27, KIAA0226, and smoking associated with overall survival of early-stage NSCLC.
      Title: Epigenome-wide three-way interaction study identifies a complex pattern between TRIM27, KIAA0226, and smoking associated with overall survival of early-stage NSCLC.
    4. Identification of highly potent and selective inhibitor, TIPTP, of the p22phox-Rubicon axis as a therapeutic agent for rheumatoid arthritis.
      Title: Identification of highly potent and selective inhibitor, TIPTP, of the p22phox-Rubicon axis as a therapeutic agent for rheumatoid arthritis.
    5. Hepatitis C virus enhances Rubicon expression, leading to autophagy inhibition and intracellular innate immune activation.
      Title: Hepatitis C virus enhances Rubicon expression, leading to autophagy inhibition and intracellular innate immune activation.
    6. Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
      Title: Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
    7. Rubicon as a novel substrate of HUNK.
      Title: HUNK Phosphorylates Rubicon to Support Autophagy.
    8. Rubicon (Rubcn) was identified as a negative regulator of canonical autophagy and endosomal trafficking [Review].
      Title: Rubicon: LC3-associated phagocytosis and beyond.
    9. Rubicon thus functions as an important negative regulator of the innate immune response, enhances viral replication and may play a role in viral immune evasion.
      Title: Inducible Rubicon facilitates viral replication by antagonizing interferon production.
    10. HCV, by differentially inducing the expression of Rubicon and UVRAG, temporally regulated the autophagic flux to enhance its replication.
      Title: HCV induces the expression of Rubicon and UVRAG to temporally regulate the maturation of autophagosomes and viral replication.
    Submit: New GeneRIF Correction See all GeneRIFs (20)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Autosomal recessive spinocerebellar ataxia 15
    MedGen: C3810326 OMIM: 615705 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol 3-kinase inhibitor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in immune system process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in multivesicular body sorting pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of autophagosome maturation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of autophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in phagocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    NOT colocalizes_with Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in early endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in late endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    run domain Beclin-1-interacting and cysteine-rich domain-containing protein
    Names
    RUN and cysteine rich domain containing beclin 1 interacting protein
    RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein
    baron
    beclin-1 associated RUN domain containing protein
    rundataxin

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_034153.2 RefSeqGene

      Range
      4880..85833
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1093

    mRNA and Protein(s)

    1. NM_001145642.5 → NP_001139114.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform 1

      See identical proteins and their annotated locations for NP_001139114.1

      Status: REVIEWED

      Source sequence(s)
      AC024560, AI796534, D86979, DB036516
      Consensus CDS
      CCDS46987.1
      UniProtKB/TrEMBL
      H0Y6E6
      Related
      ENSP00000273582.5, ENST00000273582.9
      Conserved Domains (3) summary
      pfam05109
      Location:137 → 402
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam13901
      Location:692 → 892
      zf-RING_9; Putative zinc-RING and/or ribbon
      cd17686
      Location:1 → 130
      RUN_RUBCN; RUN domain found in Run domain Beclin-1-interacting and cysteine-rich domain-containing protein (RUBCN) and similar proteins

    2. NM_001346873.2 → NP_001333802.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC024560
      UniProtKB/TrEMBL
      A0A9L9PY84, H0Y6E6
      Related
      ENSP00000516727.1, ENST00000707076.1

    3. NM_014687.4 → NP_055502.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform 2

      See identical proteins and their annotated locations for NP_055502.1

      Status: REVIEWED

      Source sequence(s)
      AC024560, AI796534, BC033615, D86979, HY003277
      Consensus CDS
      CCDS43195.1
      UniProtKB/Swiss-Prot
      Q92622, Q96CK5
      UniProtKB/TrEMBL
      H0Y6E6
      Related
      ENSP00000296343.5, ENST00000296343.10
      Conserved Domains (2) summary
      smart00593
      Location:122 → 182
      RUN; domain involved in Ras-like GTPase signaling
      pfam13901
      Location:737 → 937
      zf-RING_9; Putative zinc-RING and/or ribbon

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      197668867..197749820 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006713831.5 → XP_006713894.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X6

      See identical proteins and their annotated locations for XP_006713894.1

      UniProtKB/TrEMBL
      H0Y6E6
      Conserved Domains (1) summary
      pfam13901
      Location:610 → 810
      zf-RING_9; Putative zinc-RING and/or ribbon

    2. XM_047449268.1 → XP_047305224.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X3

      UniProtKB/TrEMBL
      H0Y6E6

    3. XM_017007543.2 → XP_016863032.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X5

      UniProtKB/TrEMBL
      H0Y6E6
      Conserved Domains (2) summary
      pfam13901
      Location:596 → 792
      zf-RING_9; Putative zinc-RING and/or ribbon
      pfam15782
      Location:22 → 143
      GREB1; Gene regulated by oestrogen in breast cancer

    4. XM_006713828.4 → XP_006713891.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X2

      UniProtKB/TrEMBL
      H0Y6E6
      Conserved Domains (2) summary
      smart00593
      Location:122 → 182
      RUN; domain involved in Ras-like GTPase signaling
      pfam13901
      Location:762 → 962
      zf-RING_9; Putative zinc-RING and/or ribbon

    5. XM_005269374.4 → XP_005269431.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X4

      UniProtKB/TrEMBL
      H0Y6E6
      Related
      ENSP00000405115.1, ENST00000413360.5
      Conserved Domains (2) summary
      smart00593
      Location:122 → 182
      RUN; domain involved in Ras-like GTPase signaling
      pfam13901
      Location:752 → 952
      zf-RING_9; Putative zinc-RING and/or ribbon

    6. XM_006713827.4 → XP_006713890.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X1

      UniProtKB/TrEMBL
      H0Y6E6
      Conserved Domains (2) summary
      smart00593
      Location:122 → 182
      RUN; domain involved in Ras-like GTPase signaling
      pfam13901
      Location:777 → 977
      zf-RING_9; Putative zinc-RING and/or ribbon

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      200401254..200482196 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348515.1 → XP_054204490.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X3

      UniProtKB/TrEMBL
      H0Y6E6

    2. XM_054348517.1 → XP_054204492.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X6

      UniProtKB/TrEMBL
      H0Y6E6

    3. XM_054348514.1 → XP_054204489.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X2

      UniProtKB/TrEMBL
      H0Y6E6

    4. XM_054348516.1 → XP_054204491.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X4

      UniProtKB/TrEMBL
      H0Y6E6

    5. XM_054348513.1 → XP_054204488.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X1

      UniProtKB/TrEMBL
      H0Y6E6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92622.4 GenPept UniProtKB/Swiss-Prot:Q92622

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