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

Summary

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

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_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

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General gene information

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Markers

RH131014 (e-PCR)
- UniSTS:214297

RH140075 (e-PCR)
- UniSTS:222156

RH133780 (e-PCR)
- UniSTS:217063

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)

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

NC_086021.1 Reference GRCr8

Range

97640923..97667617 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063282967.1 → XP_063139037.1 DNA damage-binding protein 2 isoform X3
XM_006234498.5 → XP_006234560.2 DNA damage-binding protein 2 isoform X2
XM_063282966.1 → XP_063139036.1 DNA damage-binding protein 2 isoform X1
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 ...
XM_063282968.1 → XP_063139038.1 DNA damage-binding protein 2 isoform X4