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RUBCN rubicon autophagy regulator [ Homo sapiens (human) ]

Gene ID: 9711, updated on 13-Aug-2022

Summary

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

See RUBCN in Genome Data Viewer
Location:
3q29
Exon count:
24
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (197668867..197749820, complement)
110 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 uncharacterized LOC124909481 Neighboring gene keratinocyte proline-rich protein-like Neighboring gene PPP4R2 pseudogene 4 Neighboring gene uncharacterized LOC124906331 Neighboring gene microRNA 922 Neighboring gene Sharpr-MPRA regulatory region 8415 Neighboring gene Sharpr-MPRA regulatory region 6653 Neighboring gene forty-two-three domain containing 1 Neighboring gene leucine rich repeats and calponin homology domain containing 3 Neighboring gene uncharacterized LOC124909482 Neighboring gene uncharacterized LOC105374310 Neighboring gene ribosomal protein L17 pseudogene 18

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phosphatidylinositol phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
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
PubMed 
located_in early endosome IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
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
PubMed 
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

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_001145642.5NP_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/Swiss-Prot
    Q92622
    Related
    ENSP00000273582.5, ENST00000273582.9
    Conserved Domains (3) summary
    pfam05109
    Location:137402
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    pfam13901
    Location:692892
    zf-RING_9; Putative zinc-RING and/or ribbon
    cd17686
    Location:1130
    RUN_RUBCN; RUN domain found in Run domain Beclin-1-interacting and cysteine-rich domain-containing protein (RUBCN) and similar proteins
  2. NM_001346873.2NP_001333802.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC024560
  3. NM_014687.4NP_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
    Q8N4U6
    Related
    ENSP00000296343.5, ENST00000296343.10
    Conserved Domains (2) summary
    smart00593
    Location:122182
    RUN; domain involved in Ras-like GTPase signaling
    pfam13901
    Location:737937
    zf-RING_9; Putative zinc-RING and/or ribbon

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_006713831.5XP_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

    Conserved Domains (1) summary
    pfam13901
    Location:610810
    zf-RING_9; Putative zinc-RING and/or ribbon
  2. XM_047449268.1XP_047305224.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X3

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

    Conserved Domains (2) summary
    pfam13901
    Location:596792
    zf-RING_9; Putative zinc-RING and/or ribbon
    pfam15782
    Location:22143
    GREB1; Gene regulated by oestrogen in breast cancer
  4. XM_006713828.4XP_006713891.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X2

    Conserved Domains (2) summary
    smart00593
    Location:122182
    RUN; domain involved in Ras-like GTPase signaling
    pfam13901
    Location:762962
    zf-RING_9; Putative zinc-RING and/or ribbon
  5. XM_005269374.4XP_005269431.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X4

    Related
    ENSP00000405115.1, ENST00000413360.5
    Conserved Domains (2) summary
    smart00593
    Location:122182
    RUN; domain involved in Ras-like GTPase signaling
    pfam13901
    Location:752952
    zf-RING_9; Putative zinc-RING and/or ribbon
  6. XM_006713827.4XP_006713890.1  run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X1

    Conserved Domains (2) summary
    smart00593
    Location:122182
    RUN; domain involved in Ras-like GTPase signaling
    pfam13901
    Location:777977
    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)