U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Zbed4 zinc finger, BED type containing 4 [ Mus musculus (house mouse) ]

    Gene ID: 223773, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Zbed4provided by MGI
    Official Full Name
    zinc finger, BED type containing 4provided by MGI
    Primary source
    MGI:MGI:2682302
    See related
    Ensembl:ENSMUSG00000034333 AllianceGenome:MGI:2682302
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    1700009F06Rik
    Summary
    Enables DNA-binding transcription activator activity, RNA polymerase II-specific; RNA binding activity; and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. Is expressed in several structures, including adipose tissue; alimentary system; genitourinary system; immune system; and nervous system. Orthologous to human ZBED4 (zinc finger BED-type containing 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thymus adult (RPKM 12.7), testis adult (RPKM 9.3) and 28 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Zbed4 in Genome Data Viewer
    Location:
    15 E3; 15 44.24 cM
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (88635856..88668719)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (88751662..88784516)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 35997 Neighboring gene bromodomain containing 1 Neighboring gene STARR-seq mESC enhancer starr_39439 Neighboring gene STARR-positive B cell enhancer ABC_E9918 Neighboring gene STARR-positive B cell enhancer ABC_E5507 Neighboring gene STARR-seq mESC enhancer starr_39444 Neighboring gene STARR-positive B cell enhancer ABC_E391 Neighboring gene ALG12 alpha-1,6-mannosyltransferase Neighboring gene cysteine-rich with EGF-like domains 2

    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: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. ZBED4, a BED-type zinc-finger protein in the cones of the human retina. Saghizadeh M, et al. Invest Ophthalmol Vis Sci, 2009 Aug. PMID 19369242, Free PMC Article
    2. Sequence-specific binding of recombinant Zbed4 to DNA: insights into Zbed4 participation in gene transcription and its association with other proteins. Mokhonov VV, et al. PLoS One, 2012. PMID 22693546, Free PMC Article
    3. ZBED4, a cone and Müller cell protein in human retina, has a different cellular expression in mouse. Saghizadeh M, et al. Mol Vis, 2011. PMID 21850176, Free PMC Article
    4. Telencephalic embryonic subtractive sequences: a unique collection of neurodevelopmental genes. Bulfone A, et al. J Neurosci, 2005 Aug 17. PMID 16107646, Free PMC Article
    5. Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, et al. DNA Res, 2003 Feb 28. PMID 12693553

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. structural and functional properties of Zbed4
      Title: Sequence-specific binding of recombinant Zbed4 to DNA: insights into Zbed4 participation in gene transcription and its association with other proteins.
    2. The patterns of spatial and temporal expression of Zbed4 in the mouse retina suggest a possible involvement of this protein in retinal morphogenesis and Muller cell function.
      Title: ZBED4, a cone and Müller cell protein in human retina, has a different cellular expression in mouse.
    Submit: New GeneRIF Correction

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (2) 

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC59429

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in photoreceptor inner segment 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 4
    Names
    zinc finger, BED domain containing 4

    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_181412.4 → NP_852077.1  zinc finger BED domain-containing protein 4

      See identical proteins and their annotated locations for NP_852077.1

      Status: VALIDATED

      Source sequence(s)
      AC117700
      Consensus CDS
      CCDS27731.1
      UniProtKB/Swiss-Prot
      Q3UPJ9, Q80TV3, Q80WQ9, Q8R329
      Related
      ENSMUSP00000035437.9, ENSMUST00000041297.15
      Conserved Domains (2) summary
      pfam02892
      Location:460 → 506
      zf-BED; BED zinc finger
      pfam05699
      Location:1085 → 1134
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000081.7 Reference GRCm39 C57BL/6J

      Range
      88635856..88668719
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006520840.5 → XP_006520903.1  zinc finger BED domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_006520903.1

      UniProtKB/Swiss-Prot
      Q3UPJ9, Q80TV3, Q80WQ9, Q8R329
      Conserved Domains (2) summary
      pfam02892
      Location:460 → 506
      zf-BED; BED zinc finger
      pfam05699
      Location:1085 → 1134
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region

    2. XM_006520841.5 → XP_006520904.1  zinc finger BED domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_006520904.1

      UniProtKB/Swiss-Prot
      Q3UPJ9, Q80TV3, Q80WQ9, Q8R329
      Conserved Domains (2) summary
      pfam02892
      Location:460 → 506
      zf-BED; BED zinc finger
      pfam05699
      Location:1085 → 1134
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region

    3. XM_030248511.1 → XP_030104371.1  zinc finger BED domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      Q3UPJ9, Q80TV3, Q80WQ9, Q8R329
      Conserved Domains (2) summary
      pfam02892
      Location:460 → 506
      zf-BED; BED zinc finger
      pfam05699
      Location:1085 → 1134
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q80WQ9.1 GenPept UniProtKB/Swiss-Prot:Q80WQ9

    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