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ZBED1 zinc finger BED-type containing 1 [ Homo sapiens (human) ]

Gene ID: 9189, updated on 5-Mar-2024

Summary

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Official Symbol
ZBED1provided by HGNC
Official Full Name
zinc finger BED-type containing 1provided by HGNC
Primary source
HGNC:HGNC:447
See related
Ensembl:ENSG00000214717 Ensembl:ENSG00000292345 MIM:300178; AllianceGenome:HGNC:447
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
ALTE; DREF; TRAMP; hDREF
Summary
This gene is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes. It was earlier identified as a gene with similarity to Ac transposable elements, however, was found not to have transposase activity. Later studies show that this gene product is localized in the nucleus and functions as a transcription factor. It binds to DNA elements found in the promoter regions of several genes related to cell proliferation, such as histone H1, hence may have a role in regulating genes related to cell proliferation. Alternatively spliced transcript variants with different 5' untranslated region have been found for this gene. [provided by RefSeq, Jan 2010]
Expression
Ubiquitous expression in kidney (RPKM 10.8), colon (RPKM 10.6) and 25 other tissues See more
Orthologs
all
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Genomic context

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See ZBED1 in Genome Data Viewer
Location:
X;Y
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (2486435..2500976, complement)
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (2486435..2500976, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (2099191..2113734, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (2163179..2177723, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (2404476..2419017, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (2354476..2369017, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985677 Neighboring gene H3K27ac hESC enhancer GRCh37_chrY:1956524-1957311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2035872-2036372 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrY:1993758-1994466 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chrY:2010123-2010650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2170834-2171344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2171345-2171853 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2180646-2181480 Neighboring gene dehydrogenase/reductase X-linked Neighboring gene uncharacterized LOC124905239 Neighboring gene NANOG-H3K27ac hESC enhancers GRCh37_chrX:2309773-2310384 and GRCh37_chrY:2259846-2260410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2311094-2311904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2467730-2468457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2501116-2501616 Neighboring gene H3K4me1 hESC enhancers GRCh37_chrX:2501617-2502117 and GRCh37_chrY:2451809-2452308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:2476579-2477103 Neighboring gene long intergenic non-protein coding RNA 3112 Neighboring gene microRNA 6089

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985677 Neighboring gene H3K27ac hESC enhancer GRCh37_chrY:1956524-1957311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2035872-2036372 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrY:1993758-1994466 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chrY:2010123-2010650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2170834-2171344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2171345-2171853 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2180646-2181480 Neighboring gene dehydrogenase/reductase X-linked Neighboring gene uncharacterized LOC124905239 Neighboring gene NANOG-H3K27ac hESC enhancers GRCh37_chrX:2309773-2310384 and GRCh37_chrY:2259846-2260410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2311094-2311904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2467730-2468457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2501116-2501616 Neighboring gene H3K4me1 hESC enhancers GRCh37_chrX:2501617-2502117 and GRCh37_chrY:2451809-2452308 Neighboring gene long intergenic non-protein coding RNA 3112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:2476579-2477103 Neighboring gene long intergenic non-protein coding RNA 102 Neighboring gene microRNA 6089 Neighboring gene CD99 molecule pseudogene 1

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. ZBED1 Regulates Genes Important for Multiple Biological Processes of the Placenta. Johansen S, et al. Genes (Basel), 2022 Jan 12. PMID 35052473, Free PMC Article
  2. Human DREF/ZBED1 is a nuclear protein widely expressed in multiple cell types derived from all three primary germ layers. Hansen SV, et al. PLoS One, 2018. PMID 30304065, Free PMC Article
  3. Identification of a human homologue of the DREF transcription factor with a potential role in regulation of the histone H1 gene. Ohshima N, et al. J Biol Chem, 2003 Jun 20. PMID 12663651
  4. A novel pseudoautosomal human gene encodes a putative protein similar to Ac-like transposases. Esposito T, et al. Hum Mol Genet, 1999 Jan. PMID 9887332
  5. hDREF regulates cell proliferation and expression of ribosomal protein genes. Yamashita D, et al. Mol Cell Biol, 2007 Mar. PMID 17220279, Free PMC Article

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ZBED1 Regulates Genes Important for Multiple Biological Processes of the Placenta.
    Title: ZBED1 Regulates Genes Important for Multiple Biological Processes of the Placenta.
  2. The pseudoautosomal region of human X and Y chromosome encoded ZBED1 protein was predicted to interact with at least 10 proteins encoded on the somatic chromosomes.
    Title: Bioinformatics Annotation of Human Y Chromosome-Encoded Protein Pathways and Interactions.
  3. ZBED1 is not a cell proliferation-associated factor such as Drosophila DREF, and our study adds to the cumulative understanding of the functions of ZBED1 in human cells and tissues.
    Title: Human DREF/ZBED1 is a nuclear protein widely expressed in multiple cell types derived from all three primary germ layers.
  4. These findings identify DREF as a novel adenovirus E1A C terminus binding partner and provide evidence supporting a role for DREF in viral replication.
    Title: Adenovirus E1A targets the DREF nuclear factor to regulate virus gene expression, DNA replication, and growth.
  5. expression of hDREF/KIAA0785 may have a role in regulation of human genes related to cell proliferation
    Title: Identification of a human homologue of the DREF transcription factor with a potential role in regulation of the histone H1 gene.
  6. self-association of hDREF via the hATC domain is necessary for its nuclear accumulation and DNA binding.
    Title: Human DNA replication-related element binding factor (hDREF) self-association via hATC domain is necessary for its nuclear accumulation and DNA binding.
  7. hDREF is an important transcription factor for cell proliferation which plays roles in cell cycle-dependent regulation of a number of ribosomal protein genes
    Title: hDREF regulates cell proliferation and expression of ribosomal protein genes.
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

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

  • KIAA0785

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables SUMO ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables SUMO transferase activity EXP
Inferred from Experiment
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription coactivator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription coactivator activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables transcription coregulator activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation by host of viral genome replication IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein autosumoylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein sumoylation TAS
Traceable Author Statement
more info
  
involved_in regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in PML body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in centrosome IDA
Inferred from Direct Assay
more info
  
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in nuclear membrane IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
E3 SUMO-protein ligase ZBED1
Names
Ac-like transposable element
BED-type zinc finger domain-containing protein 1
DNA replication-related element binding factor
dREF homolog
zinc finger BED domain-containing protein 1

NCBI Reference Sequences (RefSeq)

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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_016364.1 RefSeqGene

    Range
    4992..19533
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001171135.2 → NP_001164606.1  E3 SUMO-protein ligase ZBED1

    See identical proteins and their annotated locations for NP_001164606.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' terminal exon compared to variant 1. Variants 1-3 encode the same protein.
    Source sequence(s)
    AB018328, AC079176, BC015030, BM980254, DA625185
    Consensus CDS
    CCDS14118.1
    UniProtKB/Swiss-Prot
    O96006, Q96BY4
    Related
    ENSP00000370616.3, ENSP00000518653.1, ENST00000381218.8, ENST00000711169.1
    Conserved Domains (3) summary
    pfam02892
    Location:23 → 72
    zf-BED; BED zinc finger
    pfam05699
    Location:571 → 650
    Dimer_Tnp_hAT; hAT family C-terminal dimerization region
    pfam14372
    Location:412 → 480
    DUF4413; Domain of unknown function (DUF4413)

  2. NM_001171136.2 → NP_001164607.1  E3 SUMO-protein ligase ZBED1

    See identical proteins and their annotated locations for NP_001164607.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript. Variants 1-3 encode the same protein.
    Source sequence(s)
    AB018328, AC079176, BC015030, BM980254, DA625185
    Consensus CDS
    CCDS14118.1
    UniProtKB/Swiss-Prot
    O96006, Q96BY4
    Related
    ENSP00000498725.1, ENSP00000518654.1, ENST00000652001.1, ENST00000711171.1
    Conserved Domains (3) summary
    pfam02892
    Location:23 → 72
    zf-BED; BED zinc finger
    pfam05699
    Location:571 → 650
    Dimer_Tnp_hAT; hAT family C-terminal dimerization region
    pfam14372
    Location:412 → 480
    DUF4413; Domain of unknown function (DUF4413)

  3. NM_004729.4 → NP_004720.1  E3 SUMO-protein ligase ZBED1

    See identical proteins and their annotated locations for NP_004720.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate acceptor splice site at the 3' terminal exon compared to variant 1. Variants 1-3 encode the same protein.
    Source sequence(s)
    AB018328, AC079176, BM980254, DA625185
    Consensus CDS
    CCDS14118.1
    UniProtKB/Swiss-Prot
    O96006, Q96BY4
    Related
    ENSP00000370620.2, ENSP00000518656.1, ENST00000381222.8, ENST00000711173.1
    Conserved Domains (3) summary
    pfam02892
    Location:23 → 72
    zf-BED; BED zinc finger
    pfam05699
    Location:571 → 650
    Dimer_Tnp_hAT; hAT family C-terminal dimerization region
    pfam14372
    Location:412 → 480
    DUF4413; Domain of unknown function (DUF4413)

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    2486435..2500976 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    2486435..2500976 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    2099191..2113734 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    2163179..2177723 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O96006.1 GenPept UniProtKB/Swiss-Prot:O96006

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