Ddb2 damage specific DNA binding protein 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ddb2provided by MGI
Official Full Name: damage specific DNA binding protein 2provided by MGI
Primary source: MGI:MGI:1355314
See related: Ensembl:ENSMUSG00000002109 AllianceGenome:MGI:1355314
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: 2610043A19Rik
Summary: Predicted to contribute to damaged DNA binding activity and ubiquitin-protein transferase activity. Involved in DNA damage response and cellular response to UV. Acts upstream of or within pyrimidine dimer repair. Part of Cul4A-RING E3 ubiquitin ligase complex. Used to study xeroderma pigmentosum group E. 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: Ubiquitous expression in mammary gland adult (RPKM 18.6), spleen adult (RPKM 15.8) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 E1; 2 50.56 cM

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (91041924..91067465, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (91211545..91237132, complement)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DDB2 plays a critical role in suppressing development of colon cancer at early stage by regulating Wnt signaling. Mice genetically deficient in DDB2 exhibited increased susceptibility to colon tumor development in a manner associated with higher abundance of the Wnt receptor-expressing cells and greater activation of the downstream Wnt pathway.
Title: DDB2 Is a Novel Regulator of Wnt Signaling in Colon Cancer.
UVRAG is a regulator of CRL4(DDB2)-mediated nucleotide excision repair and its expression levels may influence melanoma predisposition.
Title: Autophagic UVRAG Promotes UV-Induced Photolesion Repair by Activation of the CRL4(DDB2) E3 Ligase.
Results indicate a transcriptional regulatory pathway of DDB2 that is directly linked to the mechanisms that suppress metastasis of colon cancer.
Title: DDB2 suppresses epithelial-to-mesenchymal transition in colon cancer.
Data indicate that poly(ADP-ribose) polymerase-1 (PARP-1)collaborates with DNA-binding protein 2 (DDB2) to increase the efficiency of the lesion recognition step of global genomic subpathway of NER (GG-NER).
Title: Role of poly(ADP-ribose) polymerase-1 in the removal of UV-induced DNA lesions by nucleotide excision repair.
the anti-proliferative and the pro-senescence pathways of DDB2 and p21 are critical protection mechanisms against skin malignancies.
Title: p21 cooperates with DDB2 protein in suppression of ultraviolet ray-induced skin malignancies.
mouse keratinocytes express sufficient levels of UV-DDB for efficient repair of photolesions and efficient protection against Ultraviolet rays (UV)-induced skin cancer at physiological relevant ultraviolet rays exposure.
Title: Differential activity of UV-DDB in mouse keratinocytes and fibroblasts: impact on DNA repair and UV-induced skin cancer.
results provide evidence for a new regulatory loop involving the NER protein DDB2, Mdm2, and p21(Waf1/Cip1) that is critical in deciding cell fate (apoptosis or arrest) upon DNA damage.
Title: DDB2 decides cell fate following DNA damage.
provide genetic evidence linking the regulation of p21(Waf1/Cip1) to the nucleotide excision repair activity of DDB2
Title: The xeroderma pigmentosum group E gene product DDB2 activates nucleotide excision repair by regulating the level of p21Waf1/Cip1.
results indicate the bulk of DDB2 interacts with lesions independent of XPC & there is little interaction between the two recognition proteins on damaged DNA; propose a scenario in which DDB2 prepares UV-damaged chromatin for assembly of the NER complex
Title: Dynamic in vivo interaction of DDB2 E3 ubiquitin ligase with UV-damaged DNA is independent of damage-recognition protein XPC.
Ddb2 heterozygosity can facilitate tumor development as a haploinsufficient tumor suppressor
Title: Ddb2 is a haploinsufficient tumor suppressor and controls spontaneous germ cell apoptosis.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI131584 (e-PCR)
- UniSTS:207351

C86680 (e-PCR)
- UniSTS:207352

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
contributes_to damaged DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables damaged DNA binding	IEA Inferred from Electronic Annotation more info
contributes_to damaged DNA binding	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin-protein transferase activity	IEA Inferred from Electronic Annotation more info
contributes_to ubiquitin-protein transferase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA damage response	EXP Inferred from Experiment more info	PubMed
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in cellular response to UV	EXP Inferred from Experiment more info	PubMed
involved_in cellular response to UV	ISO Inferred from Sequence Orthology more info
involved_in cellular response to UV	ISS Inferred from Sequence or Structural Similarity more info
involved_in nucleotide-excision repair	ISO Inferred from Sequence Orthology more info
involved_in nucleotide-excision repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein autoubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein autoubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein polyubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein polyubiquitination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pyrimidine dimer repair	IMP Inferred from Mutant Phenotype more info	PubMed
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	EXP Inferred from Experiment more info	PubMed
part_of Cul4A-RING E3 ubiquitin ligase complex	ISO Inferred from Sequence Orthology more info
part_of Cul4B-RING E3 ubiquitin ligase complex	IEA Inferred from Electronic Annotation 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
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
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
is_active_in site of DNA damage	ISS Inferred from Sequence or Structural Similarity 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)

NM_001362705.1 → NP_001349634.1 DNA damage-binding protein 2 isoform 2

Status: VALIDATED

Source sequence(s)

AK158770, BC099410, CK627126

UniProtKB/TrEMBL

Q4FZK4

Conserved Domains (1) summary

sd00039
Location:114 → 151

7WD40; WD40 repeat [structural motif]
NM_028119.5 → NP_082395.2 DNA damage-binding protein 2 isoform 1

See identical proteins and their annotated locations for NP_082395.2

Status: VALIDATED

Source sequence(s)

BC058589, BU515611, CK627126

Consensus CDS

CCDS16428.1

UniProtKB/Swiss-Prot

Q99J79

Related

ENSMUSP00000028696.5, ENSMUST00000028696.5

Conserved Domains (3) summary

COG2319
Location:58 → 431

WD40; WD40 repeat [General function prediction only]

sd00039
Location:115 → 154

7WD40; WD40 repeat [structural motif]

cl02567
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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

91041924..91067465 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036157313.1 → XP_036013206.1 DNA damage-binding protein 2 isoform X1

Conserved Domains (2) summary

sd00039
Location:115 → 154

7WD40; WD40 repeat [structural motif]

cl29593
Location:115 → 293

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 ...