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

Gene ID: 393599, updated on 2-Nov-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, Nov 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

Gene LinkOut

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