RUBCNL rubicon like autophagy enhancer [Homo sapiens (human)] - Gene

Summary

Official Symbol: RUBCNLprovided by HGNC
Official Full Name: rubicon like autophagy enhancerprovided by HGNC
Primary source: HGNC:HGNC:20420
See related: Ensembl:ENSG00000102445 MIM:620175; AllianceGenome:HGNC:20420
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: PACER; C13orf18; KIAA0226L
Summary: This gene encodes a cysteine-rich protein that contains a putative zinc-RING and/or ribbon domain. The encoded protein is related to Run domain Beclin-1-interacting and cysteine-rich domain-containing protein, which plays a role in endocytic trafficking and autophagy. In cervical cancer cell lines, this gene is expressed at low levels and may function as a tumor suppressor. Promoter hypermethylation of this gene is observed in cervical cancer cell lines and tissue derived from human patients. [provided by RefSeq, Mar 2017]
Expression: Biased expression in lymph node (RPKM 14.1), spleen (RPKM 8.4) and 13 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 13q14.13

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (46334681..46390042, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (45555685..45611047, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (46908816..46964177, complement)

Chromosome 13 - NC_000013.11 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
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?

Tumor-derived lactate promotes resistance to bevacizumab treatment by facilitating autophagy enhancer protein RUBCNL expression through histone H3 lysine 18 lactylation (H3K18la) in colorectal cancer.
Title: Tumor-derived lactate promotes resistance to bevacizumab treatment by facilitating autophagy enhancer protein RUBCNL expression through histone H3 lysine 18 lactylation (H3K18la) in colorectal cancer.
MYC-activated CERS6-AS1 sponges miR-6838-5p and regulates the expression of RUBCNL in colorectal cancer.
Title: MYC-activated CERS6-AS1 sponges miR-6838-5p and regulates the expression of RUBCNL in colorectal cancer.
mTORC1 and GSK3-TIP60 signaling converge to modulate autophagosome maturation and lipid metabolism through Pacer.
Title: Pacer Is a Mediator of mTORC1 and GSK3-TIP60 Signaling in Regulation of Autophagosome Maturation and Lipid Metabolism.
Pacer localizes to autophagic structures and positively regulates autophagosome maturation.
Title: Pacer Mediates the Function of Class III PI3K and HOPS Complexes in Autophagosome Maturation by Engaging Stx17.
MethyLight data demonstrated that C13orf18 and C1orf166 could not be considered as specific, sensitive and suitable prognostic biomarkers in cervical dysplasia related Papillomavirus Infections.
Title: C13orf18 and C1orf166 (MULAN) DNA genes methylation are not associated with cervical cancer and precancerous lesions of human papillomavirus genotypes in Iranian women.
Re-activation of C13ORF18 led to partial demethylation of the C13ORF18 promoter and decreased repressive histone methylation.
Title: Functional validation of putative tumor suppressor gene C13ORF18 in cervical cancer by Artificial Transcription Factors.
Data suggest that the four-gene methylation panel might provide an alternative triage test after primary high-risk papillomavirus (hr-HPV) testing.
Title: A four-gene methylation marker panel as triage test in high-risk human papillomavirus positive patients.
Methylation of C13orf18 in cervical scrapings is strongly associated with high-grade cervical intraepithelial neoplasia and cervical cancer.
Title: Methylation markers for CCNA1 and C13ORF18 are strongly associated with high-grade cervical intraepithelial neoplasia and cervical cancer in cervical scrapings.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Screening for replication of genome-wide SNP associations in sporadic ALS.
Observational study of gene-disease association. (HuGE Navigator)
Title: Replication of a genome-wide case-control study of esophageal squamous cell carcinoma.

Submit: New GeneRIF Correction

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

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

RH98403 (e-PCR)
- UniSTS:86669

SHGC-58563 (e-PCR)
- UniSTS:94399

RH44948 (e-PCR)
- UniSTS:75747

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables phosphatidylinositol phosphate binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol-3-phosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol-4-phosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol-5-phosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in autophagosome maturation	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagosome maturation	IDA Inferred from Direct Assay more info	PubMed
involved_in autophagosome-endosome fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagosome-endosome fusion	IDA Inferred from Direct Assay more info	PubMed
involved_in autophagosome-lysosome fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagosome-lysosome fusion	IDA Inferred from Direct Assay more info	PubMed
involved_in lipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in regulation of glycogen metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of lipid metabolic process	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in autophagosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in autophagosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic vesicle	IEA Inferred from Electronic Annotation more info
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: protein associated with UVRAG as autophagy enhancer

Names: KIAA0226 like; RUN and cysteine rich domain containing beclin 1 interacting protein like; protein RUBCNL-like; protein Rubicon-like; rubicon like autophagy regulator

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_053064.2 RefSeqGene

Range

7790..60361

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001286761.2 → NP_001273690.1 protein associated with UVRAG as autophagy enhancer isoform a

See identical proteins and their annotated locations for NP_001273690.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2 and 8 encode the same isoform (a).

Source sequence(s)

AK093073, AL139801, BC004495, CD701535, DB050136

Consensus CDS

CCDS31970.2

UniProtKB/Swiss-Prot

A8KAG9, A8XR19, B3KS87, Q5W051, Q5W053, Q6PJ74, Q6PK94, Q86XH7, Q8N5J6, Q9H714

UniProtKB/TrEMBL

A0A6Q8PFX0

Related

ENSP00000374558.3, ENST00000389908.7

Conserved Domains (1) summary

pfam13901
Location:451 → 646

zf-RING_9; Putative zinc-RING and/or ribbon
NM_001286762.3 → NP_001273691.1 protein associated with UVRAG as autophagy enhancer isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AK025215, AL139801, BC032311, CD701535, DC330997

Consensus CDS

CCDS66543.1

UniProtKB/Swiss-Prot

Q9H714

Related

ENSP00000368064.3, ENST00000378787.7

Conserved Domains (1) summary

pfam13901
Location:451 → 543

zf-RING_9; Putative zinc-RING and/or ribbon
NM_001286763.3 → NP_001273692.1 protein associated with UVRAG as autophagy enhancer isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks a portion of the 5' coding region and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded isoform (c) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AK293034, AL139801, BC043488, CD701535, DC330997

Consensus CDS

CCDS66545.1

UniProtKB/TrEMBL

A0A6Q8PFX0

Related

ENSP00000368061.4, ENST00000378784.8

Conserved Domains (1) summary

pfam13901
Location:384 → 579

zf-RING_9; Putative zinc-RING and/or ribbon
NM_001286764.3 → NP_001273693.1 protein associated with UVRAG as autophagy enhancer isoform d

See identical proteins and their annotated locations for NP_001273693.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) has a shorter N-terminus than isoform 1.

Source sequence(s)

AK293034, AL139801, CD701535

Consensus CDS

CCDS66542.1

UniProtKB/TrEMBL

B7Z6E4

Related

ENSP00000485932.1, ENST00000631139.2

Conserved Domains (1) summary

pfam13901
Location:316 → 511

zf-RING_9; Putative zinc-RING and/or ribbon
NM_001286765.3 → NP_001273694.1 protein associated with UVRAG as autophagy enhancer isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks a portion of the 5' coding region and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded isoform (e) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AK300183, AL139801, BC043488, CD701535, DC330997

Consensus CDS

CCDS66544.1

UniProtKB/TrEMBL

B7Z6E4, B7ZBN5, G8JLB1

Related

ENSP00000368057.4, ENST00000378781.7

Conserved Domains (1) summary

pfam13901
Location:294 → 489

zf-RING_9; Putative zinc-RING and/or ribbon
NM_001286766.3 → NP_001273695.1 protein associated with UVRAG as autophagy enhancer isoform f

Status: REVIEWED

Description

Transcript Variant: This variant (7) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (f) has a shorter N-terminus than isoform 1.

Source sequence(s)

AK025215, AK307854, AL139801, CD701535, DC330997

Consensus CDS

CCDS73569.1

UniProtKB/TrEMBL

A0A0A0MRV7, B7Z6E4

Related

ENSP00000368074.3, ENST00000378797.6

Conserved Domains (1) summary

pfam13901
Location:236 → 431

zf-RING_9; Putative zinc-RING and/or ribbon
NM_001349772.2 → NP_001336701.1 protein associated with UVRAG as autophagy enhancer isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (8) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 8 encode the same isoform (a).

Source sequence(s)

AL139801, CD701535

Consensus CDS

CCDS31970.2

UniProtKB/Swiss-Prot

A8KAG9, A8XR19, B3KS87, Q5W051, Q5W053, Q6PJ74, Q6PK94, Q86XH7, Q8N5J6, Q9H714

UniProtKB/TrEMBL

A0A6Q8PFX0

Related

ENSP00000502015.1, ENST00000676307.1

Conserved Domains (1) summary

pfam13901
Location:451 → 646

zf-RING_9; Putative zinc-RING and/or ribbon
NM_025113.5 → NP_079389.2 protein associated with UVRAG as autophagy enhancer isoform a

See identical proteins and their annotated locations for NP_079389.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1, 2 and 8 encode the same isoform (a).

Source sequence(s)

AL139801, CD701535

Consensus CDS

CCDS31970.2

UniProtKB/Swiss-Prot

A8KAG9, A8XR19, B3KS87, Q5W051, Q5W053, Q6PJ74, Q6PK94, Q86XH7, Q8N5J6, Q9H714

UniProtKB/TrEMBL

A0A6Q8PFX0

Related

ENSP00000396935.1, ENST00000429979.6

Conserved Domains (1) summary

pfam13901
Location:451 → 646

zf-RING_9; Putative zinc-RING and/or ribbon