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RUBCN rubicon autophagy regulator [ Homo sapiens (human) ]

Gene ID: 9711, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (197668867..197749820, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (200401254..200482196, complement)
105.20220307 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: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. 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
  2. Rubicon: LC3-associated phagocytosis and beyond. Wong SW, et al. FEBS J, 2018 Apr. PMID 29215797, Free PMC Article
  3. The Salih ataxia mutation impairs Rubicon endosomal localization. Assoum M, et al. Cerebellum, 2013 Dec. PMID 23728897
  4. 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
  5. Binding Rubicon to cross the Rubicon. Matsunaga K, et al. Autophagy, 2009 Aug. PMID 19550146

See all (60) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
    Title: Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
  6. Rubicon as a novel substrate of HUNK.
    Title: HUNK Phosphorylates Rubicon to Support Autophagy.
  7. Rubicon (Rubcn) was identified as a negative regulator of canonical autophagy and endosomal trafficking [Review].
    Title: Rubicon: LC3-associated phagocytosis and beyond.
  8. 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.
  9. 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.
  10. This study demonistrated that KIAA0226 mutation impairs Rubicon endosomal localization
    Title: The Salih ataxia mutation impairs Rubicon endosomal localization.
Submit: New GeneRIF Correction See all GeneRIFs (19)

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
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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_2023_10

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

  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

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

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

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

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

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

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