Ddb1 damage-specific DNA binding protein 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ddb1provided by RGD
Official Full Name: damage-specific DNA binding protein 1provided by RGD
Primary source: RGD:621889
See related: EnsemblRapid:ENSRNOG00000020715 AllianceGenome:RGD:621889
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: Enables damaged DNA binding activity. Predicted to be involved in several processes, including UV-damage excision repair; positive regulation by virus of viral protein levels in host cell; and positive regulation of gluconeogenesis. Predicted to act upstream of or within several processes, including Wnt signaling pathway; negative regulation of apoptotic process; and proteasomal protein catabolic process. Predicted to be located in cytoplasm 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 nucleolus and site of double-strand break. 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: Biased expression in Adrenal (RPKM 711.3), Kidney (RPKM 619.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q43

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (216677810..216703605)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (207252890..207278685)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (226657561..226683356)

Chromosome 1 - NC_086019.1 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

role in UV-damaged-DNA recognition activity in mammalian tissues and cell lines
Title: Identification of rat DDB1, a putative DNA repair protein, and functional correlation with its damaged-DNA recognition activity.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH128925 (e-PCR)
- UniSTS:212233

RH129228 (e-PCR)
- UniSTS:212536

Gene Ontology Provided by RGD

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
enables damaged DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
contributes_to damaged DNA binding	ISO Inferred from Sequence Orthology more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation 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 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	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	TAS Traceable Author Statement more info	PubMed
involved_in UV-damage excision repair	IEA Inferred from Electronic Annotation more info
involved_in UV-damage excision repair	ISO Inferred from Sequence Orthology more info
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of apoptotic process	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in ectopic germ cell programmed cell death	IEA Inferred from Electronic Annotation more info
acts_upstream_of ectopic germ cell programmed cell death	ISO Inferred from Sequence Orthology more info
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
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of developmental process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of developmental process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of reproductive process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of reproductive process	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gluconeogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gluconeogenesis	ISS Inferred from Sequence or Structural Similarity more info
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
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	IEA Inferred from Electronic Annotation 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	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	IEA Inferred from Electronic Annotation more info
involved_in regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in regulation of circadian rhythm	ISS Inferred from Sequence or Structural Similarity more info
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	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity 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	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	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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
located_in nucleus	IEA Inferred from Electronic Annotation 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
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: damage-specific DNA binding protein 1, 127kDa

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_171995.2 → NP_741992.2 DNA damage-binding protein 1

See identical proteins and their annotated locations for NP_741992.2

Status: VALIDATED

Source sequence(s)

CB777486, CV108212, CV111529, FM035228, FM065862, FM101956, FM131388, FN804617, FN805433, JAXUCZ010000001

UniProtKB/Swiss-Prot

Q9ESW0

UniProtKB/TrEMBL

A6I047, G3V8T4

Related

ENSRNOP00000088553.1, ENSRNOT00000095970.2

Conserved Domains (2) summary

pfam03178
Location:791 → 1099

CPSF_A; CPSF A subunit region

pfam10433
Location:75 → 543

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

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

NC_086019.1 Reference GRCr8

Range

216677810..216703605

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063272772.1 → XP_063128842.1 DNA damage-binding protein 1 isoform X1
XM_039089596.1 → XP_038945524.1 DNA damage-binding protein 1 isoform X3

UniProtKB/Swiss-Prot

Q9ESW0

Related

ENSRNOP00000028188.5, ENSRNOT00000028188.9

Conserved Domains (2) summary

pfam03178
Location:796 → 1104

CPSF_A; CPSF A subunit region

pfam10433
Location:75 → 548

MMS1_N; Mono-functional DNA-alkylating methyl methanesulfonate N-term
XM_063272773.1 → XP_063128843.1 DNA damage-binding protein 1 isoform X2

Related

ENSRNOP00000105255.1, ENSRNOT00000172347.1