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. Pro... See more...

Aliases for RUBCNL Gene

Aliases for RUBCNL Gene

  • Rubicon Like Autophagy Enhancer 2 3 5
  • RUN And Cysteine Rich Domain Containing Beclin 1 Interacting Protein Like 2 3
  • Protein Associated With UVRAG As Autophagy Enhancer 3 4
  • Protein Rubicon-Like 3 4
  • KIAA0226 Like 2 3
  • KIAA0226L 3 4
  • C13orf18 3 4
  • Chromosome 13 Open Reading Frame 18 2
  • Rubicon Like Autophagy Regulator 3
  • Protein RUBCNL-Like 3
  • PACER 3
  • Pacer 4

External Ids for RUBCNL Gene

Previous HGNC Symbols for RUBCNL Gene

  • C13orf18
  • KIAA0226L

Summaries for RUBCNL Gene

Entrez Gene Summary for RUBCNL Gene

  • 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]

GeneCards Summary for RUBCNL Gene

RUBCNL (Rubicon Like Autophagy Enhancer) is a Protein Coding gene. Diseases associated with RUBCNL include Cervical Cancer and Cervix Uteri Carcinoma In Situ. An important paralog of this gene is RUBCN.

UniProtKB/Swiss-Prot Summary for RUBCNL Gene

  • Regulator of autophagy that promotes autophagosome maturation by facilitating the biogenesis of phosphatidylinositol 3-phosphate (PtdIns(3)P) in late steps of autophagy (PubMed:28306502, PubMed:30704899). Acts by antagonizing RUBCN, thereby stimulating phosphatidylinositol 3-kinase activity of the PI3K/PI3KC3 complex (PubMed:28306502). Following anchorage to the autophagosomal SNARE STX17, promotes the recruitment of PI3K/PI3KC3 and HOPS complexes to the autophagosome to regulate the fusion specificity of autophagosomes with late endosomes/lysosomes (PubMed:28306502). Binds phosphoinositides phosphatidylinositol 3-phosphate (PtdIns(3)P), 4-phosphate (PtdIns(4)P) and 5-phosphate (PtdIns(5)P) (PubMed:28306502). In addition to its role in autophagy, acts as a regulator of lipid and glycogen homeostasis (By similarity). May act as a tumor suppressor (Probable).

Additional gene information for RUBCNL Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RUBCNL Gene

Genomics for RUBCNL Gene

GeneHancer (GH) Regulatory Elements for RUBCNL Gene

Promoters and enhancers for RUBCNL Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH13J046372 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 504.5 +56.0 56021 18.9 ZBTB40 EP300 SIN3A TEAD4 ZFX ZBTB26 SAP30 RELA MEF2C RAD21 RUBCNL OR7E101P LINC01198 LCP1 lnc-LCP1-2 RNU2-6P lnc-LRRC63-6 RF00004-037
GH13J046437 Promoter 0.6 Ensembl 500.7 +0.2 189 1.2 POLR2G NRF1 SP1 L3MBTL2 PPP1R2P4 RUBCNL OR7E101P piR-50444-098
GH13J046163 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 8.4 +263.4 263394 21.8 ZBTB40 CTCF SIN3A EP300 ZIC2 POLR2A AFF1 RELA MEF2C TOE1 LCP1 ERICH6B RNU2-6P RUBCNL LRRC63 TPT1-AS1 ZC3H13 piR-34822-077 lnc-CPB2-2 lnc-CPB2-3
GH13J046552 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 7 -116.2 -116211 6 ZBTB40 ZNF217 CTCF SIN3A NRF1 POLR2G ZNF639 REST ZBTB10 CLOCK LRCH1 RUBCNL LINC01198 LCP1 lnc-LRRC63-4
GH13J046654 Enhancer 1.1 Ensembl ENCODE dbSUPER 7.2 -218.4 -218411 5.2 TCF12 EP300 TRIM22 OSR2 NR3C1 MAFK ZNF513 BATF GATA3 STAT3 RUBCNL LRCH1 piR-41245-072 ENSG00000278462
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RUBCNL on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RUBCNL

Genomic Locations for RUBCNL Gene

Genomic Locations for RUBCNL Gene
chr13:46,342,000-46,438,190
(GRCh38/hg38)
Size:
96,191 bases
Orientation:
Minus strand
chr13:46,916,136-47,012,325
(GRCh37/hg19)
Size:
96,190 bases
Orientation:
Minus strand

Genomic View for RUBCNL Gene

Genes around RUBCNL on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RUBCNL Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RUBCNL Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RUBCNL Gene

Proteins for RUBCNL Gene

  • Protein details for RUBCNL Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H714-PACER_HUMAN
    Recommended name:
    Protein associated with UVRAG as autophagy enhancer
    Protein Accession:
    Q9H714
    Secondary Accessions:
    • A8KAG9
    • A8XR19
    • B3KS87
    • Q5W051
    • Q5W053
    • Q6PJ74
    • Q6PK94
    • Q86XH7
    • Q8N5J6

    Protein attributes for RUBCNL Gene

    Size:
    662 amino acids
    Molecular mass:
    73457 Da
    Quaternary structure:
    • Interacts with UVRAG; the interaction is direct and promotes association with the PI3K/PI3KC3 and HOPS complexes (PubMed:28306502). Interacts with STX17 (PubMed:28306502, PubMed:30704899).
    Miscellaneous:
    • [Isoform 3]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    • [Isoform 4]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Alternative splice isoforms for RUBCNL Gene

neXtProt entry for RUBCNL Gene

Post-translational modifications for RUBCNL Gene

  • Phosphorylated by MTOR at Ser-157 under nutrient-rich conditions (PubMed:30704899). Phosphorylation prevents acetylation by KAT5/TIP60 and impairs RUBCNL/PACER function and autophagosome maturation (PubMed:30704899). Under autophagy induction, Phosphorylation by MTOR is repressed, enabling acetylation by KAT5/TIP60 (PubMed:30704899).
  • Acetylated by KAT5/TIP60 under autophagy induction, promoting autophagosome maturation and lipid metabolism (PubMed:30704899). Acetylation is prevented by phosphorylation by MTOR (PubMed:30704899). Lys-483 and Lys-573 constitute the key sites for tuning function in autophagy (PubMed:30704899).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RUBCNL Gene

Domains & Families for RUBCNL Gene

Gene Families for RUBCNL Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RUBCNL Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RUBCNL Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ75517 (A8KAG9_HUMAN)
genes like me logo Genes that share domains with RUBCNL: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RUBCNL Gene

Function for RUBCNL Gene

Molecular function for RUBCNL Gene

UniProtKB/Swiss-Prot Function:
Regulator of autophagy that promotes autophagosome maturation by facilitating the biogenesis of phosphatidylinositol 3-phosphate (PtdIns(3)P) in late steps of autophagy (PubMed:28306502, PubMed:30704899). Acts by antagonizing RUBCN, thereby stimulating phosphatidylinositol 3-kinase activity of the PI3K/PI3KC3 complex (PubMed:28306502). Following anchorage to the autophagosomal SNARE STX17, promotes the recruitment of PI3K/PI3KC3 and HOPS complexes to the autophagosome to regulate the fusion specificity of autophagosomes with late endosomes/lysosomes (PubMed:28306502). Binds phosphoinositides phosphatidylinositol 3-phosphate (PtdIns(3)P), 4-phosphate (PtdIns(4)P) and 5-phosphate (PtdIns(5)P) (PubMed:28306502). In addition to its role in autophagy, acts as a regulator of lipid and glycogen homeostasis (By similarity). May act as a tumor suppressor (Probable).
UniProtKB/Swiss-Prot Induction:
Up-regulated by epigenetic drugs, such as azacitidine, and artificial transcription factors (ATFs)-induced treatments in cervical carcinoma cell lines.

Phenotypes From GWAS Catalog for RUBCNL Gene

Gene Ontology (GO) - Molecular Function for RUBCNL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 28306502
GO:0008289 lipid binding IEA --
GO:0010314 phosphatidylinositol-5-phosphate binding IDA 28306502
GO:0032266 phosphatidylinositol-3-phosphate binding IDA 28306502
GO:0070273 phosphatidylinositol-4-phosphate binding IDA 28306502
genes like me logo Genes that share ontologies with RUBCNL: view
genes like me logo Genes that share phenotypes with RUBCNL: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RUBCNL

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RUBCNL Gene

Localization for RUBCNL Gene

Subcellular locations from UniProtKB/Swiss-Prot for RUBCNL Gene

Cytoplasmic vesicle, autophagosome membrane; Peripheral membrane protein. Note=Associates with late autophagic structure (PubMed:28306502). Recruitment to autophagosome membrane is promoted by autophagic stimuli (PubMed:28306502). {ECO:0000269 PubMed:28306502}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RUBCNL gene
Compartment Confidence
cytosol 3
nucleus 2
plasma membrane 1
cytoskeleton 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RUBCNL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000421 autophagosome membrane IDA 28306502
GO:0016020 membrane IEA --
GO:0031410 cytoplasmic vesicle IEA --
genes like me logo Genes that share ontologies with RUBCNL: view

Pathways & Interactions for RUBCNL Gene

PathCards logo

SuperPathways for RUBCNL Gene

No Data Available

Gene Ontology (GO) - Biological Process for RUBCNL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006914 autophagy IEA --
GO:0019216 regulation of lipid metabolic process ISS --
GO:0061909 autophagosome-lysosome fusion IDA 28306502
GO:0061910 autophagosome-endosome fusion IDA 28306502
genes like me logo Genes that share ontologies with RUBCNL: view

No data available for Pathways by source and SIGNOR curated interactions for RUBCNL Gene

Drugs & Compounds for RUBCNL Gene

No Compound Related Data Available

Transcripts for RUBCNL Gene

mRNA/cDNA for RUBCNL Gene

8 REFSEQ mRNAs :
22 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RUBCNL

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RUBCNL Gene

No ASD Table

Relevant External Links for RUBCNL Gene

GeneLoc Exon Structure for
RUBCNL

Expression for RUBCNL Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RUBCNL

mRNA Expression by UniProt/SwissProt for RUBCNL Gene:

Q9H714-PACER_HUMAN
Tissue specificity: Expressed weakly in cervical carcinoma cell lines.

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for RUBCNL Gene

Orthologs for RUBCNL Gene

This gene was present in the common ancestor of chordates.

Orthologs for RUBCNL Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KIAA0226L 31 30
  • 99.35 (n)
OneToOne
dog
(Canis familiaris)
Mammalia KIAA0226L 31 30
  • 83.23 (n)
OneToOne
cow
(Bos Taurus)
Mammalia KIAA0226L 31 30
  • 80.38 (n)
OneToOne
mouse
(Mus musculus)
Mammalia 5031414D18Rik 31 30
  • 73.04 (n)
OneToOne
Rubcnl 17
rat
(Rattus norvegicus)
Mammalia RGD1304929 30
  • 72.17 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia KIAA0226L 31
  • 55 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia KIAA0226L 31
  • 50 (a)
OneToOne
chicken
(Gallus gallus)
Aves KIAA0226L 31 30
  • 65.86 (n)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.15213 30
zebrafish
(Danio rerio)
Actinopterygii si:ch211-260b17.6 31
  • 55 (a)
OneToOne
Species where no ortholog for RUBCNL was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RUBCNL Gene

ENSEMBL:
Gene Tree for RUBCNL (if available)
TreeFam:
Gene Tree for RUBCNL (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RUBCNL: view image

Paralogs for RUBCNL Gene

Paralogs for RUBCNL Gene

genes like me logo Genes that share paralogs with RUBCNL: view

Variants for RUBCNL Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RUBCNL Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
715525 Benign: not provided 46,371,941(-) C/G MISSENSE_VARIANT,INTRON_VARIANT
rs193920942 Uncertain Significance: Malignant tumor of prostate 46,359,610(-) G/A NONSENSE
rs1408184 - p.Gly152Arg

Additional dbSNP identifiers (rs#s) for RUBCNL Gene

Structural Variations from Database of Genomic Variants (DGV) for RUBCNL Gene

Variant ID Type Subtype PubMed ID
dgv223e201 CNV deletion 23290073
esv3631982 CNV loss 21293372
esv3631983 CNV loss 21293372
esv3631985 CNV loss 21293372
esv3631986 CNV loss 21293372
nsv1045198 CNV gain 25217958
nsv455876 CNV gain 19166990
nsv561581 CNV gain 21841781

Variation tolerance for RUBCNL Gene

Residual Variation Intolerance Score: 93.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.74; 83.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RUBCNL Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RUBCNL

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RUBCNL Gene

Disorders for RUBCNL Gene

MalaCards: The human disease database

(3) MalaCards diseases for RUBCNL Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
cervical cancer
  • cervical cancer, somatic
cervix uteri carcinoma in situ
  • carcinoma in situ of cervix
uterus carcinoma in situ
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RUBCNL

genes like me logo Genes that share disorders with RUBCNL: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RUBCNL Gene

Publications for RUBCNL Gene

  1. Pacer Mediates the Function of Class III PI3K and HOPS Complexes in Autophagosome Maturation by Engaging Stx17. (PMID: 28306502) Cheng X … Sun Q (Molecular cell 2017) 2 3 4 54
  2. Functional validation of putative tumor suppressor gene C13ORF18 in cervical cancer by Artificial Transcription Factors. (PMID: 23522960) Huisman C … Rots MG (Molecular oncology 2013) 2 3 4 54
  3. Pacer Is a Mediator of mTORC1 and GSK3-TIP60 Signaling in Regulation of Autophagosome Maturation and Lipid Metabolism. (PMID: 30704899) Cheng X … Sun Q (Molecular cell 2019) 3 4 54
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54

Products for RUBCNL Gene

Sources for RUBCNL Gene