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    ZRANB1 zinc finger RANBP2-type containing 1 [ Homo sapiens (human) ]

    Gene ID: 54764, updated on 7-Apr-2024

    Summary

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    Official Symbol
    ZRANB1provided by HGNC
    Official Full Name
    zinc finger RANBP2-type containing 1provided by HGNC
    Primary source
    HGNC:HGNC:18224
    See related
    Ensembl:ENSG00000019995 MIM:611749; AllianceGenome:HGNC:18224
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TRABID
    Summary
    Enables K63-linked polyubiquitin modification-dependent protein binding activity and thiol-dependent deubiquitinase. Involved in several processes, including positive regulation of Wnt signaling pathway; protein deubiquitination; and regulation of cell morphogenesis. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in adrenal (RPKM 10.7), testis (RPKM 10.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    10q26.13
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (124916894..124988189)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (125823167..125869209)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (126630692..126676758)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126489987-126490541 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:126490542-126491095 Neighboring gene abraxas 2, BRISC complex subunit Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126553027-126553526 Neighboring gene nucleophosmin 1 pseudogene 31 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2921 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4188 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_10909 Neighboring gene uncharacterized LOC124902520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126688910-126689410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126691205-126691746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126691747-126692287 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126696421-126696926 Neighboring gene C-terminal binding protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126715397-126715939 Neighboring gene microRNA 4296

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. ZRANB1 enhances stem-cell-like features and accelerates tumor progression by regulating Sox9-mediated USP22/Wnt/β-catenin pathway in colorectal cancer. Miao D, et al. Cell Signal, 2022 Feb. PMID 34798260
    2. Deubiquitinase ZRANB1 drives hepatocellular carcinoma progression through SP1-LOXL2 axis. Li Q, et al. Am J Cancer Res, 2021. PMID 34765294, Free PMC Article
    3. An ankyrin-repeat ubiquitin-binding domain determines TRABID's specificity for atypical ubiquitin chains. Licchesi JD, et al. Nat Struct Mol Biol, 2011 Dec 11. PMID 22157957, Free PMC Article
    4. The E3 ubiquitin ligase HECTD1 contributes to cell proliferation through an effect on mitosis. Vaughan N, et al. Sci Rep, 2022 Aug 1. PMID 35915203, Free PMC Article
    5. Trabid inhibits hepatocellular carcinoma growth and metastasis by cleaving RNF8-induced K63 ubiquitination of Twist1. Zhu Y, et al. Cell Death Differ, 2019 Jan. PMID 29748601, Free PMC Article

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Trabid patient mutations impede the axonal trafficking of adenomatous polyposis coli to disrupt neurite growth.
      Title: Trabid patient mutations impede the axonal trafficking of adenomatous polyposis coli to disrupt neurite growth.
    2. The deubiquitinase ZRANB1 is an E3 ubiquitin ligase for SLC7A11 and regulates ferroptotic resistance.
      Title: The deubiquitinase ZRANB1 is an E3 ubiquitin ligase for SLC7A11 and regulates ferroptotic resistance.
    3. TRABID targets DDB2 for deubiquitination to promote proliferation of hepatocellular carcinoma cells.
      Title: TRABID targets DDB2 for deubiquitination to promote proliferation of hepatocellular carcinoma cells.
    4. ZRANB1 enhances stem-cell-like features and accelerates tumor progression by regulating Sox9-mediated USP22/Wnt/beta-catenin pathway in colorectal cancer.
      Title: ZRANB1 enhances stem-cell-like features and accelerates tumor progression by regulating Sox9-mediated USP22/Wnt/β-catenin pathway in colorectal cancer.
    5. The deubiquitinase TRABID stabilizes the K29/K48-specific E3 ubiquitin ligase HECTD1.
      Title: The deubiquitinase TRABID stabilizes the K29/K48-specific E3 ubiquitin ligase HECTD1.
    6. Knockdown of Trabid promoted hepatocellular carcinoma growth and metastasis via regulating Twist1 K63-ubiquitination.
      Title: Trabid inhibits hepatocellular carcinoma growth and metastasis by cleaving RNF8-induced K63 ubiquitination of Twist1.
    7. ZRANB1 binds, deubiquitinates, and stabilizes EZH2. Depletion of ZRANB1 in breast cancer cells results in EZH2 destabilization and growth inhibition.
      Title: ZRANB1 Is an EZH2 Deubiquitinase and a Potential Therapeutic Target in Breast Cancer.
    8. Data show that the ankyrin-repeat ubiquitin-binding domain is crucial for TRABID efficiency and linkage specificity.
      Title: An ankyrin-repeat ubiquitin-binding domain determines TRABID's specificity for atypical ubiquitin chains.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp762P2216

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables K63-linked polyubiquitin modification-dependent protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables K63-linked polyubiquitin modification-dependent protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cysteine-type deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables polyubiquitin modification-dependent protein 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 Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of Wnt signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein K29-linked deubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein K29-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K33-linked deubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein K33-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K63-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K63-linked deubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein deubiquitination involved in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein deubiquitination involved in ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ubiquitin thioesterase ZRANB1
    Names
    TRAF-binding domain-containing protein
    TRAF-binding protein domain
    hTrabid
    zinc finger Ran-binding domain-containing protein 1
    zinc finger, RAN-binding domain containing 1
    NP_060050.2
    XP_006717970.1
    XP_047281339.1
    XP_047281340.1
    XP_047281341.1

    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.

    mRNA and Protein(s)

    1. NM_017580.3 → NP_060050.2  ubiquitin thioesterase ZRANB1

      See identical proteins and their annotated locations for NP_060050.2

      Status: VALIDATED

      Source sequence(s)
      AJ252060, AL731571, AL832925
      Consensus CDS
      CCDS7642.1
      UniProtKB/Swiss-Prot
      B4DZ98, D3DRF4, Q5SQP6, Q69YK3, Q9UGI0
      Related
      ENSP00000352676.4, ENST00000359653.4
      Conserved Domains (4) summary
      smart00547
      Location:152 → 175
      ZnF_RBZ; Zinc finger domain
      sd00029
      Location:88 → 107
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam02338
      Location:438 → 586
      OTU; OTU-like cysteine protease
      pfam18418
      Location:246 → 341
      AnkUBD; Ankyrin ubiquitin-binding domain

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      124916894..124988189
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006717907.3 → XP_006717970.1  ubiquitin thioesterase ZRANB1 isoform X1

      See identical proteins and their annotated locations for XP_006717970.1

      Conserved Domains (4) summary
      smart00547
      Location:178 → 201
      ZnF_RBZ; Zinc finger domain
      sd00029
      Location:114 → 133
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam02338
      Location:464 → 612
      OTU; OTU-like cysteine protease
      pfam18418
      Location:272 → 367
      AnkUBD; Ankyrin ubiquitin-binding domain

    2. XM_047425383.1 → XP_047281339.1  ubiquitin thioesterase ZRANB1 isoform X2

      UniProtKB/Swiss-Prot
      B4DZ98, D3DRF4, Q5SQP6, Q69YK3, Q9UGI0

    3. XM_047425384.1 → XP_047281340.1  ubiquitin thioesterase ZRANB1 isoform X2

      UniProtKB/Swiss-Prot
      B4DZ98, D3DRF4, Q5SQP6, Q69YK3, Q9UGI0

    4. XM_047425385.1 → XP_047281341.1  ubiquitin thioesterase ZRANB1 isoform X2

      UniProtKB/Swiss-Prot
      B4DZ98, D3DRF4, Q5SQP6, Q69YK3, Q9UGI0

    RNA

    1. XR_007061968.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      125823167..125869209
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UGI0.2 GenPept UniProtKB/Swiss-Prot:Q9UGI0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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