U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 58486, updated on 10-Dec-2024

    Summary

    Go to the top of the page Help
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See ZBED5 in Genome Data Viewer
    Location:
    11p15.4
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (10852706..10858053, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (10937686..10943033, complement)
    RS_2024_09 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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    Go to the top of the pageHelp

    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 (17) 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

    Go to the top of the page Help

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    zinc finger BED domain-containing protein 5
    Names
    transposon-derived Buster1 transposase-like protein

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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.

    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_2024_08

    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.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools