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

Gene ID: 80183, updated on 2-Mar-2021

Summary

Official Symbol
RUBCNLprovided by HGNC
Official Full Name
rubicon like autophagy enhancerprovided by HGNC
Primary source
HGNC:HGNC:20420
See related
Ensembl:ENSG00000102445
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
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Genomic context

See RUBCNL in Genome Data Viewer
Location:
13q14.13
Exon count:
17
Annotation release Status Assembly Chr Location
109.20210226 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (46334681..46390042, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (46908816..46964177, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene leucine rich repeat containing 63 Neighboring gene uncharacterized LOC105370194 Neighboring gene ABITRAM pseudogene 1 Neighboring gene long intergenic non-protein coding RNA 563 Neighboring gene RNA, U2 small nuclear 6, pseudogene Neighboring gene RNA, U6 small nuclear 68, pseudogene Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 2 pseudogene 4

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

Clone Names

  • FLJ21562, FLJ43762

Gene Ontology Provided by GOA

Function Evidence Code Pubs
phosphatidylinositol phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylinositol-3-phosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol-4-phosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol-5-phosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
autophagosome maturation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
autophagosome maturation IDA
Inferred from Direct Assay
more info
PubMed 
autophagosome-endosome fusion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
autophagosome-endosome fusion IDA
Inferred from Direct Assay
more info
PubMed 
autophagosome-lysosome fusion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
autophagosome-lysosome fusion IDA
Inferred from Direct Assay
more info
PubMed 
lipid metabolic process IEA
Inferred from Electronic Annotation
more info
 
regulation of glycogen metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of lipid metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
autophagosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
autophagosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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)

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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_053064.1 RefSeqGene

    Range
    5001..53304
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001286761.2NP_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
    Q9H714
    Related
    ENSP00000374558.3, ENST00000389908.7
    Conserved Domains (1) summary
    pfam13901
    Location:451646
    zf-RING_9; Putative zinc-RING and/or ribbon
  2. NM_001286762.3NP_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:451543
    zf-RING_9; Putative zinc-RING and/or ribbon
  3. NM_001286763.3NP_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/Swiss-Prot
    Q9H714
    Related
    ENSP00000368061.4, ENST00000378784.8
    Conserved Domains (1) summary
    pfam13901
    Location:384579
    zf-RING_9; Putative zinc-RING and/or ribbon
  4. NM_001286764.3NP_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/Swiss-Prot
    Q9H714
    Related
    ENSP00000485932.1, ENST00000631139.2
    Conserved Domains (1) summary
    pfam13901
    Location:316511
    zf-RING_9; Putative zinc-RING and/or ribbon
  5. NM_001286765.3NP_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
    B7ZBN5
    Related
    ENSP00000368057.4, ENST00000378781.7
    Conserved Domains (1) summary
    pfam13901
    Location:294489
    zf-RING_9; Putative zinc-RING and/or ribbon
  6. NM_001286766.3NP_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
    Related
    ENSP00000368074.3, ENST00000378797.6
    Conserved Domains (1) summary
    pfam13901
    Location:236431
    zf-RING_9; Putative zinc-RING and/or ribbon
  7. NM_001349772.2NP_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
    Related
    ENSP00000502015.1, ENST00000676307.1
    Conserved Domains (1) summary
    pfam13901
    Location:451646
    zf-RING_9; Putative zinc-RING and/or ribbon
  8. NM_025113.5NP_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
    Q9H714
    Related
    ENSP00000396935.1, ENST00000429979.5
    Conserved Domains (1) summary
    pfam13901
    Location:451646
    zf-RING_9; Putative zinc-RING and/or ribbon

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210226

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    46334681..46390042 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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