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

    Gene ID: 58486, updated on 3-Nov-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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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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. USP9X deubiquitinates and stabilizes CDC123 to promote breast carcinogenesis through regulating cell cycle. Song N, et al. Mol Carcinog, 2023 Oct. PMID 37314216
    2. Comparative analysis of the recently discovered hAT transposon TcBuster in human cells. Woodard LE, et al. PLoS One, 2012. PMID 23166581, Free PMC Article
    3. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Smit AF. Curr Opin Genet Dev, 1999 Dec. PMID 10607616
    4. 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
    5. 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

    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

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See Variation Viewer (GRCh37.p13)

    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_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
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