ddb2 damage-specific DNA binding protein 2 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: ddb2provided by ZNC
Official Full Name: damage-specific DNA binding protein 2provided by ZNC
Primary source: ZFIN:ZDB-GENE-050419-169
See related: Ensembl:ENSDARG00000041140 AllianceGenome:ZFIN:ZDB-GENE-050419-169
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: si:dkey-45f10.3
Summary: Predicted to enable DNA binding activity. Predicted to contribute to damaged DNA binding activity. Predicted to be involved in nucleotide-excision repair and response to UV. Predicted to act upstream of or within DNA damage response. Predicted to be located in chromosome. Predicted to be part of Cul4-RING E3 ubiquitin ligase complex. Predicted to be active in nucleus and site of DNA damage. Is expressed in central nervous system and neurons. 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, Jan 2025]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 18

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	18	NC_007129.7 (20468157..20479334)
105	previous assembly	GRCz10 (GCF_000002035.5)	18	NC_007129.6 (20479091..20490268)

Chromosome 18 - NC_007129.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Regulation of ddb2 expression in blind cavefish and zebrafish reveals plasticity in the control of sunlight-induced DNA damage repair.
Title: Regulation of ddb2 expression in blind cavefish and zebrafish reveals plasticity in the control of sunlight-induced DNA damage repair.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
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

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within DNA repair	IEA Inferred from Electronic Annotation more info
involved_in nucleotide-excision repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in response to UV	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of Cul4-RING E3 ubiquitin ligase complex	IEA Inferred from Electronic Annotation more info
located_in chromosome	IEA Inferred from Electronic Annotation 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 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_001083061.1 → NP_001076530.1 DNA damage-binding protein 2

Status: PROVISIONAL

Source sequence(s)

BX942814

UniProtKB/Swiss-Prot

Q1LUF7, Q1LUF8, Q2YDS1

UniProtKB/TrEMBL

A0A8M1NDN8, Z4YI04

Related

ENSDARP00000091438.4, ENSDART00000100665.6

Conserved Domains (3) summary

COG2319
Location:64 → 431

WD40; WD40 repeat [General function prediction only]

sd00039
Location:116 → 156

7WD40; WD40 repeat [structural motif]

cl02567
Location:105 → 420

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_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007129.7 Reference GRCz11 Primary Assembly

Range

20468157..20479334

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005159034.5 → XP_005159091.1 DNA damage-binding protein 2 isoform X1

UniProtKB/Swiss-Prot

Q1LUF7, Q1LUF8, Q2YDS1

UniProtKB/TrEMBL

A0A8M2B5L4

Related

ENSDARP00000145040.1, ENSDART00000180370.1

Conserved Domains (3) summary

COG2319
Location:64 → 437

WD40; WD40 repeat [General function prediction only]

sd00039
Location:116 → 156

7WD40; WD40 repeat [structural motif]

cl02567
Location:105 → 426

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 ...