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    ddb1 damage-specific DNA binding protein 1 [ Danio rerio (zebrafish) ]

    Gene ID: 393599, updated on 9-Dec-2024

    Summary

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    Official Symbol
    ddb1provided by ZNC
    Official Full Name
    damage-specific DNA binding protein 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-1272
    See related
    AllianceGenome:ZFIN:ZDB-GENE-040426-1272
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    zgc:63840
    Summary
    Predicted to enable nucleic acid binding activity. Acts upstream of or within negative regulation of apoptotic process and regulation of cell cycle process. Predicted to be active in nucleus and site of double-strand break. Is expressed in blastomere; endoderm; nervous system; pharyngeal arch; and somite. Human ortholog(s) of this gene implicated in communication disorder. Orthologous to human DDB1 (damage specific DNA binding protein 1). [provided by Alliance of Genome Resources, Dec 2024]
    Annotation information
    Annotation category: partial on reference assembly
    Orthologs
    human mouse all
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    Genomic context

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    See ddb1 in Genome Data Viewer
    Location:
    chromosome: 18
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 18 NC_007129.7 (50826591..50839096, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 18 NC_007129.6 (50803251..50808968)

    Chromosome 18 - NC_007129.7Genomic Context describing neighboring genes Neighboring gene tetraspanin 4a Neighboring gene uncharacterized LOC137488356 Neighboring gene uncharacterized LOC137488355 Neighboring gene pyruvate dehydrogenase phosphatase regulatory subunit Neighboring gene fibulin-7

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Loss of DDB1 Leads to Transcriptional p53 Pathway Activation in Proliferating Cells, Cell Cycle Deregulation, and Apoptosis in Zebrafish Embryos. Hu Z, et al. PLoS One, 2015. PMID 26225764, Free PMC Article
    2. Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes. Can H, et al. BMC Genomics, 2020 Jul 8. PMID 32640983, Free PMC Article
    3. Proteome dynamics in neutrophils of adult zebrafish upon chemically-induced inflammation. Singh SK, et al. Fish Shellfish Immunol, 2014 Sep. PMID 25014315
    4. Large-scale generation and phenotypic characterization of zebrafish CRISPR mutants of DNA repair genes. Shin U, et al. DNA Repair (Amst), 2021 Nov. PMID 34390914
    5. Selection of reliable biomarkers from PCR array analyses using relative distance computational model: methodology and proof-of-concept study. Liu C, et al. PLoS One, 2013. PMID 24349563, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC63840

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA damage response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of cell cycle process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in site of double-strand break IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    DNA damage-binding protein 1

    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_200626.1 → NP_956920.1  DNA damage-binding protein 1

      See identical proteins and their annotated locations for NP_956920.1

      Status: PROVISIONAL

      Source sequence(s)
      BC056837
      UniProtKB/TrEMBL
      Q6PGT6
      Conserved Domains (2) summary
      pfam03178
      Location:789 → 897
      CPSF_A; CPSF A subunit region
      pfam10433
      Location:75 → 543
      MMS1_N; Mono-functional DNA-alkylating methyl methanesulfonate N-term

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007129.7 Reference GRCz11 Primary Assembly

      Range
      50826591..50839096 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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