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    Ddb2 damage specific DNA binding protein 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 100362121, updated on 17-Aug-2024

    Summary

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    Official Symbol
    Ddb2provided by RGD
    Official Full Name
    damage specific DNA binding protein 2provided by RGD
    Primary source
    RGD:1310164
    See related
    EnsemblRapid:ENSRNOG00000014071 AllianceGenome:RGD:1310164
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to contribute to damaged DNA binding activity and ubiquitin-protein transferase activity. Predicted to be involved in UV-damage excision repair and protein ubiquitination. Predicted to act upstream of or within pyrimidine dimer repair. Predicted to be located in cell junction and nucleoplasm. Predicted to be part of Cul4B-RING E3 ubiquitin ligase complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in xeroderma pigmentosum and xeroderma pigmentosum group E. Orthologous to human DDB2 (damage specific DNA binding protein 2). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Adrenal (RPKM 55.7), Thymus (RPKM 52.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ddb2 in Genome Data Viewer
    Location:
    3q24
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (97640923..97667617, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (77185114..77207650, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (80030437..80052984, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene transfer RNA alanine (anticodon AGC) 34 Neighboring gene U6 spliceosomal RNA Neighboring gene nuclear receptor subfamily 1, group H, member 3 Neighboring gene acid phosphatase 2, lysosomal Neighboring gene protein kinase C and casein kinase substrate in neurons 3 Neighboring gene ADP-ribosylation factor GTPase activating protein 2 Neighboring gene centriolar satellite-associated tubulin polyglutamylase complex regulator 1

    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 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. Tumor-prone phenotype of the DDB2-deficient mice. Yoon T, et al. Oncogene, 2005 Jan 13. PMID 15558025, Free PMC Article
    2. Mutations specific to the xeroderma pigmentosum group E Ddb- phenotype. Nichols AF, et al. J Biol Chem, 1996 Oct 4. PMID 8798680
    3. TFIIH: when transcription met DNA repair. Compe E, et al. Nat Rev Mol Cell Biol, 2012 May 10. PMID 22572993
    4. Monoubiquitinated histone H2A destabilizes photolesion-containing nucleosomes with concomitant release of UV-damaged DNA-binding protein E3 ligase. Lan L, et al. J Biol Chem, 2012 Apr 6. PMID 22334663, Free PMC Article
    5. The ubiquitin ligase activity in the DDB2 and CSA complexes is differentially regulated by the COP9 signalosome in response to DNA damage. Groisman R, et al. Cell, 2003 May 2. PMID 12732143

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    contributes_to damaged DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    contributes_to damaged DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    contributes_to ubiquitin-protein transferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in UV-damage excision repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in cellular response to UV ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nucleotide-excision repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein autoubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein polyubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within pyrimidine dimer repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to UV IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to UV ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of Cul4-RING E3 ubiquitin ligase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of Cul4A-RING E3 ubiquitin ligase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of Cul4B-RING E3 ubiquitin ligase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell junction 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
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in site of DNA damage ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    DNA damage-binding protein 2

    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_001271346.1 → NP_001258275.1  DNA damage-binding protein 2

      See identical proteins and their annotated locations for NP_001258275.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      A0A8I5ZXK9, A6HNB7, D3ZR08
      Related
      ENSRNOP00000018998.4, ENSRNOT00000018998.10
      Conserved Domains (2) summary
      sd00039
      Location:115 → 154
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:115 → 419
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    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_086021.1 Reference GRCr8

      Range
      97640923..97667617 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063282967.1 → XP_063139037.1  DNA damage-binding protein 2 isoform X3

      UniProtKB/TrEMBL
      A0A8I5ZXK9

    2. XM_006234498.5 → XP_006234560.2  DNA damage-binding protein 2 isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZXK9

    3. XM_063282966.1 → XP_063139036.1  DNA damage-binding protein 2 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZXK9

    4. XM_039104085.2 → XP_038960013.1  DNA damage-binding protein 2 isoform X5

      Conserved Domains (2) summary
      sd00039
      Location:24 → 63
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:2 → 283
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    5. XM_063282968.1 → XP_063139038.1  DNA damage-binding protein 2 isoform X4

    Nucleotide Protein Strain
    Heading Accession and Version

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