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ZBED5 zinc finger BED-type containing 5 [ Homo sapiens (human) ]

Gene ID: 58486, updated on 5-Mar-2024

Summary

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Official Symbol
ZBED5provided by HGNC
Official Full Name
zinc finger BED-type containing 5provided by HGNC
Primary source
HGNC:HGNC:30803
See related
Ensembl:ENSG00000236287 MIM:615251; AllianceGenome:HGNC:30803
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
Buster1
Summary
This gene is unusual in that its coding sequence is mostly derived from Charlie-like DNA transposon; however, it does not appear to be an active DNA transposon as it is not flanked by terminal inverted repeats. The encoded protein is conserved among the mammalian Laurasiatheria branch. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2009]
Expression
Ubiquitous expression in lymph node (RPKM 23.1), endometrium (RPKM 21.4) and 25 other tissues See more
Orthologs
all
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Genomic context

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Location:
11p15.4
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (10852706..10858053, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (10937686..10943033, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (10874253..10879600, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 4 gamma 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4448 Neighboring gene small nucleolar RNA, C/D box 97 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4449 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4450 Neighboring gene uncharacterized LOC101928053 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10830951-10831557 Neighboring gene Sharpr-MPRA regulatory region 5180 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:10870572-10870772 Neighboring gene MPRA-validated peak1197 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4451 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10879799-10880436 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10880437-10881072 Neighboring gene ZBED5 antisense RNA 1 Neighboring gene uncharacterized LOC124902629 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:10920769-10921968

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. Comparative analysis of the recently discovered hAT transposon TcBuster in human cells. Woodard LE, et al. PLoS One, 2012. PMID 23166581, Free PMC Article
  2. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Smit AF. Curr Opin Genet Dev, 1999 Dec. PMID 10607616
  3. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. Hayward A, et al. PLoS One, 2013. PMID 23533661, Free PMC Article
  4. A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Jirawatnotai S, et al. Nature, 2011 Jun 8. PMID 21654808, Free PMC Article
  5. Genome-scale RNAi screen for host factors required for HIV replication. Zhou H, et al. Cell Host Microbe, 2008 Nov 13. PMID 18976975

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of zinc finger, BED-type containing 5 (ZBED5) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Potential readthrough

Included gene: EIF4G2

Homology

Clone Names

  • FLJ41239, FLJ44349

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
zinc finger BED domain-containing protein 5
Names
transposon-derived Buster1 transposase-like protein

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_001143667.2 → NP_001137139.1  zinc finger BED domain-containing protein 5

    See identical proteins and their annotated locations for NP_001137139.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AK315033, BQ028130, DA785416
    UniProtKB/Swiss-Prot
    B2RCC1, Q05D82, Q49AG3, Q86WW3, Q9NT24, Q9UBJ4
    UniProtKB/TrEMBL
    B3KMX8
    Related
    ENSP00000415939.2, ENST00000413761.7
    Conserved Domains (1) summary
    smart00614
    Location:117 → 160
    ZnF_BED; BED zinc finger

  2. NM_021211.4 → NP_067034.2  zinc finger BED domain-containing protein 5

    See identical proteins and their annotated locations for NP_067034.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AF205600, AK315033, BQ028130, DA785416
    UniProtKB/Swiss-Prot
    B2RCC1, Q05D82, Q49AG3, Q86WW3, Q9NT24, Q9UBJ4
    UniProtKB/TrEMBL
    B3KMX8
    Related
    ENSP00000398106.2, ENST00000432999.6
    Conserved Domains (1) summary
    smart00614
    Location:117 → 160
    ZnF_BED; BED zinc finger

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    10852706..10858053 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    10937686..10943033 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q49AG3.2 GenPept UniProtKB/Swiss-Prot:Q49AG3

Gene LinkOut

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

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