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

Gene ID: 100362121, updated on 2-Nov-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 DNA 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 Cul4A-RING E3 ubiquitin ligase complex and Cul4B-RING E3 ubiquitin ligase complex. Predicted to be active in nucleus and site of DNA damage. 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, Nov 2024]
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

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

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

  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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