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

    Gene ID: 80183, updated on 5-Mar-2024

    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
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    Genomic context

    See RUBCNL in Genome Data Viewer
    Location:
    13q14.13
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (46334681..46390042, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (45555685..45611047, complement)
    105.20220307 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 uncharacterized LOC105370194 Neighboring gene uncharacterized LOC124903170 Neighboring gene NANOG hESC enhancer GRCh37_chr13:46867593-46868094 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:46870567-46871766 Neighboring gene long intergenic non-protein coding RNA 563 Neighboring gene NANOG hESC enhancer GRCh37_chr13:46893525-46894073 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:46895131-46895630 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7694 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7695 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7696 Neighboring gene RNA, U2 small nuclear 6, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7697 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7703 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

    Clone Names

    • FLJ21562, FLJ43762

    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

    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)

    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

    1. NG_053064.2 RefSeqGene

      Range
      7790..60361
      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
      A8KAG9, A8XR19, B3KS87, Q5W051, Q5W053, Q6PJ74, Q6PK94, Q86XH7, Q8N5J6, Q9H714
      UniProtKB/TrEMBL
      A0A6Q8PFX0
      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/TrEMBL
      A0A6Q8PFX0
      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/TrEMBL
      B7Z6E4
      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
      B7Z6E4, B7ZBN5, G8JLB1
      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, B7Z6E4
      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
      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: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
      A8KAG9, A8XR19, B3KS87, Q5W051, Q5W053, Q6PJ74, Q6PK94, Q86XH7, Q8N5J6, Q9H714
      UniProtKB/TrEMBL
      A0A6Q8PFX0
      Related
      ENSP00000396935.1, ENST00000429979.6
      Conserved Domains (1) summary
      pfam13901
      Location:451646
      zf-RING_9; Putative zinc-RING and/or ribbon

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      45555685..45611047 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)