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    Zbed4 zinc finger, BED-type containing 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 315211, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Zbed4provided by RGD
    Official Full Name
    zinc finger, BED-type containing 4provided by RGD
    Primary source
    RGD:1305949
    See related
    Ensembl:ENSRNOG00000004588 AllianceGenome:RGD:1305949
    Gene type
    protein coding
    RefSeq status
    INFERRED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable RNA binding activity; identical protein binding activity; and transcription cis-regulatory region binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm and nucleoplasm. Orthologous to human ZBED4 (zinc finger BED-type containing 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 283.6), Spleen (RPKM 90.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    7q34
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (121723130..121763180)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (119846374..119883495)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (129749714..129787093)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108351525 Neighboring gene bromodomain containing 1 Neighboring gene uncharacterized LOC102547254 Neighboring gene ALG12, alpha-1,6-mannosyltransferase Neighboring gene cysteine-rich with EGF-like domains 2 Neighboring gene transfer RNA leucine (anticodon AAG) 11

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    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. 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

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger BED domain-containing protein 4
    Names
    zinc finger, BED domain containing 4

    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_001134800.4 → NP_001128272.1  zinc finger BED domain-containing protein 4

      Status: INFERRED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      D3ZUV0
      Related
      ENSRNOP00000006050.6, ENSRNOT00000006050.7
      Conserved Domains (2) summary
      pfam02892
      Location:119 → 167
      zf-BED; BED zinc finger
      pfam05699
      Location:1087 → 1163
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086025.1 Reference GRCr8

      Range
      121723130..121763180
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063263629.1 → XP_063119699.1  zinc finger BED domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      D3ZUV0

    2. XM_063263627.1 → XP_063119697.1  zinc finger BED domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      D3ZUV0

    3. XM_063263632.1 → XP_063119702.1  zinc finger BED domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      D3ZUV0

    4. XM_063263630.1 → XP_063119700.1  zinc finger BED domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      D3ZUV0

    5. XM_063263628.1 → XP_063119698.1  zinc finger BED domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      D3ZUV0

    6. XM_063263631.1 → XP_063119701.1  zinc finger BED domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      D3ZUV0
    Nucleotide Protein Strain
    Heading Accession and Version

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