RUBCN rubicon autophagy regulator [Homo sapiens (human)] - Gene

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: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: HPA RNA-seq normal tissues 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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
Title: Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
Rubicon as a novel substrate of HUNK.
Title: HUNK Phosphorylates Rubicon to Support Autophagy.
Rubicon (Rubcn) was identified as a negative regulator of canonical autophagy and endosomal trafficking [Review].
Title: Rubicon: LC3-associated phagocytosis and beyond.
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.
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

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

L17937 (e-PCR)
- UniSTS:5476

D15S1477 (e-PCR)
- UniSTS:474482

D1S1423 (e-PCR)
- UniSTS:149619

D1S1425 (e-PCR)
- UniSTS:149621

G35510 (e-PCR)
- UniSTS:44150

RH66168 (e-PCR)
- UniSTS:7862

SGC34513 (e-PCR)
- UniSTS:43476

RH99161 (e-PCR)
- UniSTS:86510

SHGC-77703 (e-PCR)
- UniSTS:35311

SHGC-77701 (e-PCR)
- UniSTS:55034

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

Go to the top of the page Help

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)

Go to the top of the page Help

NEW Try the new Transcript table

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

NG_034153.2 RefSeqGene

Range

4880..85833

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1093

mRNA and Protein(s)

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
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
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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

197668867..197749820 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_060927.1 Alternate T2T-CHM13v2.0

Range

200401254..200482196 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054348515.1 → XP_054204490.1 run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X3
XM_054348517.1 → XP_054204492.1 run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X6
XM_054348514.1 → XP_054204489.1 run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X2
XM_054348516.1 → XP_054204491.1 run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X4
XM_054348513.1 → XP_054204488.1 run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X1