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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
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Genomic context

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See ZRANB1 in Genome Data Viewer
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

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