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    DDB2 damage specific DNA binding protein 2 [ Homo sapiens (human) ]

    Gene ID: 1643, updated on 2-Nov-2024

    Summary

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    Official Symbol
    DDB2provided by HGNC
    Official Full Name
    damage specific DNA binding protein 2provided by HGNC
    Primary source
    HGNC:HGNC:2718
    See related
    Ensembl:ENSG00000134574 MIM:600811; AllianceGenome:HGNC:2718
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    XPE; DDBB; UV-DDB2
    Summary
    This gene encodes a protein that is necessary for the repair of ultraviolet light-damaged DNA. This protein is the smaller subunit of a heterodimeric protein complex that participates in nucleotide excision repair, and this complex mediates the ubiquitylation of histones H3 and H4, which facilitates the cellular response to DNA damage. This subunit appears to be required for DNA binding. Mutations in this gene cause xeroderma pigmentosum complementation group E, a recessive disease that is characterized by an increased sensitivity to UV light and a high predisposition for skin cancer development, in some cases accompanied by neurological abnormalities. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]
    Expression
    Ubiquitous expression in skin (RPKM 32.0), esophagus (RPKM 13.6) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DDB2 in Genome Data Viewer
    Location:
    11p11.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (47214454..47239217)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (47371205..47395960)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (47236005..47260768)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:47207755-47208641 Neighboring gene protein kinase C and casein kinase substrate in neurons 3 Neighboring gene microRNA 6745 Neighboring gene ribosomal protein S20 pseudogene 26 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:47231264-47231443 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47235129-47235965 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:47236089-47237288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4694 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:47270641-47270808 Neighboring gene acid phosphatase 2, lysosomal Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47280987-47281555 Neighboring gene nuclear receptor subfamily 1 group H member 3 Neighboring gene Sharpr-MPRA regulatory region 2100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3325 Neighboring gene Sharpr-MPRA regulatory region 9889 Neighboring gene MADD antisense RNA 1 Neighboring gene MAP kinase activating death domain

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Polymorphisms in DNA damage binding protein 2 (DDB2) and susceptibility of primary lung cancer in the Chinese: a case-control study. Hu Z, et al. Carcinogenesis, 2006 Jul. PMID 16522664
    2. Restoration of UV sensitivity in UV-resistant HeLa cells by antisense-mediated depletion of damaged DNA-binding protein 2 (DDB2). Sun NK, et al. FEBS Lett, 2002 Feb 13. PMID 11852074
    3. Whole Exome Sequencing allows the identification of two novel groups of Xeroderma pigmentosum in Tunisia, XP-D and XP-E: Impact on molecular diagnosis. Ben Rekaya M, et al. J Dermatol Sci, 2018 Feb. PMID 29169765
    4. UV radiation-induced SUMOylation of DDB2 regulates nucleotide excision repair. Han C, et al. Carcinogenesis, 2017 Oct 1. PMID 28981631, Free PMC Article
    5. Expression of DDB2 Protein in the Initiation, Progression, and Prognosis of Colorectal Cancer. Yang H, et al. Dig Dis Sci, 2018 Nov. PMID 30054844

    See all (198) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Brazilian XP-E siblings carrying a novel DDB2 variant developed early-onset melanoma: a case report.
      Title: Brazilian XP-E siblings carrying a novel DDB2 variant developed early-onset melanoma: a case report.
    2. Four Genes Predictive for the Severity of Hematological Damage Reveal a Similar Response after X Irradiation and Chemotherapy.
      Title: Four Genes Predictive for the Severity of Hematological Damage Reveal a Similar Response after X Irradiation and Chemotherapy.
    3. The Role of Alternative Splicing Factors, DDB2-Related Ageing and DNA Damage Repair in the Progression and Prognosis of Stomach Adenocarcinoma Patients.
      Title: The Role of Alternative Splicing Factors, DDB2-Related Ageing and DNA Damage Repair in the Progression and Prognosis of Stomach Adenocarcinoma Patients.
    4. Histone demethylase JHDM2A participates in the repair of arsenic-induced DNA damage in L-02 cells by regulating DDB2.
      Title: Histone demethylase JHDM2A participates in the repair of arsenic-induced DNA damage in L-02 cells by regulating DDB2.
    5. Global and transcription-coupled repair of 8-oxoG is initiated by nucleotide excision repair proteins.
      Title: Global and transcription-coupled repair of 8-oxoG is initiated by nucleotide excision repair proteins.
    6. Proteomic Analysis of Nuclear Hepatitis B Virus Relaxed Circular DNA-Associated Proteins Identifies UV-Damaged DNA Binding Protein as a Host Factor Involved in Covalently Closed Circular DNA Formation.
      Title: Proteomic Analysis of Nuclear Hepatitis B Virus Relaxed Circular DNA-Associated Proteins Identifies UV-Damaged DNA Binding Protein as a Host Factor Involved in Covalently Closed Circular DNA Formation.
    7. Novel mutation identified in the DDB2 gene in patients with xeroderma pigmentosum group-E.
      Title: Novel mutation identified in the DDB2 gene in patients with xeroderma pigmentosum group-E.
    8. Expanding molecular roles of UV-DDB: Shining light on genome stability and cancer.
      Title: Expanding molecular roles of UV-DDB: Shining light on genome stability and cancer.
    9. Functional impacts of the ubiquitin-proteasome system on DNA damage recognition in global genome nucleotide excision repair.
      Title: Functional impacts of the ubiquitin-proteasome system on DNA damage recognition in global genome nucleotide excision repair.
    10. Knockdown of Ubiquitin-Specific Protease 53 Enhances the Radiosensitivity of Human Cervical Squamous Cell Carcinoma by Regulating DNA Damage-Binding Protein 2.
      Title: Knockdown of Ubiquitin-Specific Protease 53 Enhances the Radiosensitivity of Human Cervical Squamous Cell Carcinoma by Regulating DNA Damage-Binding Protein 2.
    Submit: New GeneRIF Correction See all GeneRIFs (99)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Xeroderma pigmentosum, group E
    MedGen: C1848411 OMIM: 278740 GeneReviews: Xeroderma Pigmentosum
    		not available

    EBI GWAS Catalog

    Description
    Two new susceptibility loci 1q24.2 and 11p11.2 confer risk to severe acne.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpr vpr HIV-1 Vpr interferes with the interaction of DDB1 and DDB2 in cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34321

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    contributes_to damaged DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    contributes_to damaged DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables damaged DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    contributes_to ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response EXP
    Inferred from Experiment
    more info
    		 PubMed 
    involved_in DNA damage response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in UV-damage excision repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cellular response to UV EXP
    Inferred from Experiment
    more info
    		 PubMed 
    involved_in cellular response to UV ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in nucleotide-excision repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nucleotide-excision repair ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in protein autoubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein polyubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in pyrimidine dimer repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to UV IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to UV IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Cul4-RING E3 ubiquitin ligase complex IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    part_of Cul4A-RING E3 ubiquitin ligase complex EXP
    Inferred from Experiment
    more info
    		 PubMed 
    part_of Cul4B-RING E3 ubiquitin ligase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cell junction IDA
    Inferred from Direct Assay
    more info
    		  
    located_in chromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in site of DNA damage IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    DNA damage-binding protein 2
    Names
    DDB p48 subunit
    UV-damaged DNA-binding protein 2
    damage-specific DNA binding protein 2, 48kDa
    xeroderma pigmentosum group E protein

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_009365.1 RefSeqGene

      Range
      5001..29277
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_467

    mRNA and Protein(s)

    1. NM_000107.3 → NP_000098.1  DNA damage-binding protein 2 isoform WT

      See identical proteins and their annotated locations for NP_000098.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (WT) represents the longer transcript and encodes the longer isoform (WT).
      Source sequence(s)
      AA278953, U18300
      Consensus CDS
      CCDS7927.1
      UniProtKB/Swiss-Prot
      B2R875, Q76E54, Q76E55, Q76E56, Q76E57, Q92466
      Related
      ENSP00000256996.4, ENST00000256996.9
      Conserved Domains (2) summary
      sd00039
      Location:115 → 154
      7WD40; WD40 repeat [structural motif]
      cl25539
      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 ...

    2. NM_001300734.2 → NP_001287663.1  DNA damage-binding protein 2 isoform D1

      See identical proteins and their annotated locations for NP_001287663.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (D1) lacks four consecutive alternate exons compared to variant WT, without a reading frame change. The resulting isoform (D1) has the same N- and C-termini but is shorter compared to isoform WT.
      Source sequence(s)
      AA278953, AB107037, DB053816
      Consensus CDS
      CCDS73284.1
      UniProtKB/Swiss-Prot
      Q92466
      Related
      ENSP00000367863.3, ENST00000378600.7
      Conserved Domains (2) summary
      COG2319
      Location:115 → 230
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:114 → 151
      7WD40; WD40 repeat [structural motif]

    3. NM_001399874.1 → NP_001386803.1  DNA damage-binding protein 2 isoform WT

      Status: REVIEWED

      Source sequence(s)
      AC018410, AC090589, KF459540
      Consensus CDS
      CCDS7927.1
      UniProtKB/Swiss-Prot
      B2R875, Q76E54, Q76E55, Q76E56, Q76E57, Q92466

    4. NM_001399875.1 → NP_001386804.1  DNA damage-binding protein 2 isoform WT

      Status: REVIEWED

      Source sequence(s)
      AC018410, AC090589, KF459540
      Consensus CDS
      CCDS7927.1
      UniProtKB/Swiss-Prot
      B2R875, Q76E54, Q76E55, Q76E56, Q76E57, Q92466

    5. NM_001399876.1 → NP_001386805.1  DNA damage-binding protein 2 isoform D1

      Status: REVIEWED

      Source sequence(s)
      AC018410, AC090589, KF459540
      Consensus CDS
      CCDS73284.1

    6. NM_001399878.1 → NP_001386807.1  DNA damage-binding protein 2 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC018410, AC090589
      Consensus CDS
      CCDS91469.1
      Related
      ENSP00000367866.3, ENST00000378603.7

    RNA

    1. NR_174610.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018410, AC090589, KF459540

    2. NR_174611.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018410, AC090589, KF459540

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      47214454..47239217
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047426487.1 → XP_047282443.1  DNA damage-binding protein 2 isoform X1

      Related
      ENSP00000367864.3, ENST00000378601.7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      47371205..47395960
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367876.1 → XP_054223851.1  DNA damage-binding protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92466.1 GenPept UniProtKB/Swiss-Prot:Q92466

    Gene LinkOut

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