Ddb1 damage specific DNA binding protein 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ddb1provided by MGI
Official Full Name: damage specific DNA binding protein 1provided by MGI
Primary source: MGI:MGI:1202384
See related: Ensembl:ENSMUSG00000024740 AllianceGenome:MGI:1202384
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: 127kDa; p127-Ddb1
Summary: Predicted to enable several functions, including WD40-repeat domain binding activity; cullin family protein binding activity; and ubiquitin ligase complex scaffold activity. Involved in several processes, including cellular response to UV; positive regulation of gluconeogenesis; and ubiquitin-dependent protein catabolic process. Acts upstream of or within several processes, including Wnt signaling pathway; negative regulation of apoptotic process; and negative regulation of reproductive process. Part of Cul4A-RING E3 ubiquitin ligase complex. Is expressed in several structures, including blastocyst; early embryo; germ cell of gonad; otocyst; and spleen. 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]
Expression: Ubiquitous expression in placenta adult (RPKM 176.5), limb E14.5 (RPKM 97.4) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 19 A; 19 6.66 cM

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	19	NC_000085.7 (10582961..10607186)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	19	NC_000085.6 (10605568..10629828)

Chromosome 19 - NC_000085.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

Hepatocyte-specific loss of DDB1 attenuates hepatic steatosis but aggravates liver inflammation and fibrosis in MASH.
Title: Hepatocyte-specific loss of DDB1 attenuates hepatic steatosis but aggravates liver inflammation and fibrosis in MASH.
DDB1 binds histone reader BRWD3 to activate the transcriptional cascade in adipogenesis and promote onset of obesity.
Title: DDB1 binds histone reader BRWD3 to activate the transcriptional cascade in adipogenesis and promote onset of obesity.
Ddb1 Is Essential for the Expansion of CD4(+) Helper T Cells by Regulating Cell Cycle Progression and Cell Death.
Title: Ddb1 Is Essential for the Expansion of CD4(+) Helper T Cells by Regulating Cell Cycle Progression and Cell Death.
DDB1 promotes the proliferation and hypertrophy of chondrocytes during mouse skeleton development.
Title: DDB1 promotes the proliferation and hypertrophy of chondrocytes during mouse skeleton development.
Our data revealed DDB1 as an intracellular sensor of fructose intake to promote hepatic de novo lipogenesis and liver steatosis by stabilizing ChREBPalpha in a CRY1-dependent manner
Title: DDB1 E3 ligase controls dietary fructose-induced ChREBPα stabilization and liver steatosis via CRY1.
Results suggest an essential role of Ddb1 in Sertoli cell proliferation and normal remodeling of testis cords via TGFbeta pathway.
Title: DDB1 Regulates Sertoli Cell Proliferation and Testis Cord Remodeling by TGFβ Pathway.
SIRT7 inhibits TR4 degradation by deacetylation of DDB1.
Title: Sirtuin 7-dependent deacetylation of DDB1 regulates the expression of nuclear receptor TR4.
These studies identify CUL4-DDB1 complex as a novel post-translational regulator of stem and progenitor maintenance and differentiation.
Title: The CUL4-DDB1 ubiquitin ligase complex controls adult and embryonic stem cell differentiation and homeostasis.
uncovered a novel biological role for CUL4A-DDB1-CDT2 E3 ligase that regulates molecular circadian behaviors via promoting ubiquitination-dependent degradation of CRY1
Title: CUL4-DDB1-CDT2 E3 Ligase Regulates the Molecular Clock Activity by Promoting Ubiquitination-Dependent Degradation of the Mammalian CRY1.
UCH-L1 disrupts a complex between the DDB1-CUL4 ubiquitin ligase complex.
Title: Ubiquitin hydrolase UCH-L1 destabilizes mTOR complex 1 by antagonizing DDB1-CUL4-mediated ubiquitination of raptor.

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 (2)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH124722 (e-PCR)
- UniSTS:161544

RH135781 (e-PCR)
- UniSTS:209827

MARC_21157-21158:1025280537:1 (e-PCR)
- UniSTS:268494

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables WD40-repeat domain binding	IEA Inferred from Electronic Annotation more info
enables WD40-repeat domain binding	ISO Inferred from Sequence Orthology more info
enables cullin family protein binding	IEA Inferred from Electronic Annotation more info
enables cullin family protein binding	ISO Inferred from Sequence Orthology 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 damaged DNA binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
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 protein-macromolecule adaptor activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin ligase complex scaffold activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin ligase complex scaffold 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
acts_upstream_of_or_within Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in biological process involved in interaction with symbiont	IEA Inferred from Electronic Annotation more info
involved_in biological process involved in interaction with symbiont	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
acts_upstream_of ectopic germ cell programmed cell death	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epigenetic programming in the zygotic pronuclei	IEA Inferred from Electronic Annotation more info
involved_in epigenetic programming in the zygotic pronuclei	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of developmental process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of reproductive process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation by virus of viral protein levels in host cell	IEA Inferred from Electronic Annotation more info
involved_in positive regulation by virus of viral protein levels in host cell	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gluconeogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of viral genome replication	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of viral genome replication	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within proteasomal protein catabolic process	ISO Inferred from Sequence Orthology more info	PubMed
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mitotic cell cycle phase transition	IEA Inferred from Electronic Annotation more info
involved_in regulation of mitotic cell cycle phase transition	ISO Inferred from Sequence Orthology more info
involved_in rhythmic process	IEA Inferred from Electronic Annotation more info
involved_in spindle assembly involved in female meiosis	IEA Inferred from Electronic Annotation more info
involved_in spindle assembly involved in female meiosis	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in viral release from host cell	IEA Inferred from Electronic Annotation more info
involved_in viral release from host cell	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of Cul4-RING E3 ubiquitin ligase complex	IDA Inferred from Direct Assay more info	PubMed
part_of Cul4-RING E3 ubiquitin ligase complex	ISO Inferred from Sequence Orthology more info
part_of Cul4-RING E3 ubiquitin ligase complex	ISS Inferred from Sequence or Structural Similarity 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 Cul4A-RING E3 ubiquitin ligase complex	ISS Inferred from Sequence or Structural Similarity more info
part_of Cul4B-RING E3 ubiquitin ligase complex	ISO Inferred from Sequence Orthology more info
part_of Cul4B-RING E3 ubiquitin ligase complex	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
is_active_in nucleolus	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
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity 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 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

Names: DDB p127 subunit; UV-damaged DNA-binding factor; damage-specific DNA-binding protein, DNA repair; damaged-DNA recognition 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)

NM_001410219.1 → NP_001397148.1 DNA damage-binding protein 1 isoform 1

Status: VALIDATED

Source sequence(s)

AC125093, AC132247
NM_015735.3 → NP_056550.1 DNA damage-binding protein 1 isoform 2

See identical proteins and their annotated locations for NP_056550.1

Status: VALIDATED

Source sequence(s)

AC125093, AC132247

Consensus CDS

CCDS37915.1

UniProtKB/Swiss-Prot

Q3U1J4, Q3U4D0, Q3U8G3, Q3UJC4, Q99LV3, Q9QYK0, Q9WV39

UniProtKB/TrEMBL

Q91YC8

Related

ENSMUSP00000025649.9, ENSMUST00000025649.10

Conserved Domains (3) summary

COG5161
Location:13 → 1104

SFT1; Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification]

pfam03178
Location:791 → 1099

CPSF_A; CPSF A subunit region

pfam10433
Location:75 → 543

MMS1_N; Mono-functional DNA-alkylating methyl methanesulfonate N-term