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The protein encoded by this gene is the large subunit (p127) of the heterodimeric DNA damage-binding (DDB) complex while another protein (p48) forms the small subunit. This protein complex functions in nucleotide-excision repair and binds to DNA following UV damage. Defective activity of this complex causes the repair defect in patients with xeroderma pigmentosum complementatio... See more...
Aliases for DDB1 Gene
Aliases for DDB1 Gene
- Damage Specific DNA Binding Protein 1 2 3 5
- Xeroderma Pigmentosum Group E-Complementing Protein 3 4
- UV-Damaged DNA-Binding Protein 1 3 4
- UV-Damaged DNA-Binding Factor 3 4
- DNA Damage-Binding Protein 1 3 4
- DNA Damage-Binding Protein A 3 4
- HBV X-Associated Protein 1 3 4
- XPE-Binding Factor 3 4
- DDB P127 Subunit 3 4
- UV-DDB 1 3 4
- XPE-BF 3 4
External Ids for DDB1 Gene
- HGNC: 2717
- Entrez Gene: 1642
- Ensembl: ENSG00000167986
- OMIM: 600045
- UniProtKB: Q16531
Previous GeneCards Identifiers for DDB1 Gene
- GC11P063499
- GC11M062579
- GC11M061317
- GC11M060842
- GC11M060823
- GC11M061066
- GC11M057394
- GC11M061301
Summaries for DDB1 Gene
-
The protein encoded by this gene is the large subunit (p127) of the heterodimeric DNA damage-binding (DDB) complex while another protein (p48) forms the small subunit. This protein complex functions in nucleotide-excision repair and binds to DNA following UV damage. Defective activity of this complex causes the repair defect in patients with xeroderma pigmentosum complementation group E (XPE) - an autosomal recessive disorder characterized by photosensitivity and early onset of carcinomas. However, it remains for mutation analysis to demonstrate whether the defect in XPE patients is in this gene or the gene encoding the small subunit. In addition, Best vitelliform mascular dystrophy is mapped to the same region as this gene on 11q, but no sequence alternations of this gene are demonstrated in Best disease patients. The protein encoded by this gene also functions as an adaptor molecule for the cullin 4 (CUL4) ubiquitin E3 ligase complex by facilitating the binding of substrates to this complex and the ubiquitination of proteins. [provided by RefSeq, May 2012]
GeneCards Summary for DDB1 Gene
DDB1 (Damage Specific DNA Binding Protein 1) is a Protein Coding gene. Diseases associated with DDB1 include Xeroderma Pigmentosum, Complementation Group E and Xeroderma Pigmentosum Group E. Among its related pathways are Transcription-Coupled Nucleotide Excision Repair (TC-NER) and Nucleotide excision repair. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and damaged DNA binding. An important paralog of this gene is CPSF1.
UniProtKB/Swiss-Prot Summary for DDB1 Gene
-
Protein, which is both involved in DNA repair and protein ubiquitination, as part of the UV-DDB complex and DCX (DDB1-CUL4-X-box) complexes, respectively (PubMed:15448697, PubMed:14739464, PubMed:16260596, PubMed:16482215, PubMed:17079684, PubMed:16407242, PubMed:16407252, PubMed:16940174). Core component of the UV-DDB complex (UV-damaged DNA-binding protein complex), a complex that recognizes UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair (PubMed:15448697, PubMed:16260596, PubMed:16407242, PubMed:16940174). The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches (PubMed:15448697, PubMed:16260596, PubMed:16407242, PubMed:16940174). Also functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins (PubMed:14739464, PubMed:16407252, PubMed:16482215, PubMed:17079684, PubMed:25043012, PubMed:25108355, PubMed:18332868, PubMed:18381890, PubMed:19966799, PubMed:22118460, PubMed:28886238). The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1 (PubMed:14739464, PubMed:16407252, PubMed:16482215, PubMed:17079684, PubMed:25043012, PubMed:25108355, PubMed:18332868, PubMed:18381890, PubMed:19966799, PubMed:22118460). DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage (PubMed:16678110, PubMed:17041588, PubMed:16473935, PubMed:18593899). The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair (PubMed:16678110, PubMed:17041588, PubMed:16473935, PubMed:18593899). DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER (PubMed:15882621). DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication (PubMed:17041588). DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR) (PubMed:12732143). The DDB1-CUL4A-DTL E3 ligase complex regulates the circadian clock function by mediating the ubiquitination and degradation of CRY1 (PubMed:26431207). DDB1-mediated CRY1 degradation promotes FOXO1 protein stability and FOXO1-mediated gluconeogenesis in the liver (By similarity).
Additional gene information for DDB1 Gene
- HGNC(2717)
- Entrez Gene(1642)
- Ensembl(ENSG00000167986)
- OMIM(600045)
- UniProtKB(Q16531)
- Open Targets Platform(ENSG00000167986)
- Monarch Initiative
- Search for DDB1 at DataMed
- Search for DDB1 at HumanCyc
No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for DDB1 Gene
Genomics for DDB1 Gene
GeneHancer (GH) Regulatory Elements Pubs
Promoters and enhancers for DDB1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association
Download GeneHancer data from 2017 publication |
Request up-to-date GeneHancer data (full dataset)
GeneHancers around DDB1 on the GeneHancer Hub at the UCSC Golden Path
Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for DDB1
- Top Transcription factor binding sites by QIAGEN in the DDB1 gene promoter:
-
- CUTL1
- ITF-2
- NF-1
- STAT3
- Tal-1beta
- YY1
Genomic Locations for DDB1 Gene
Genomic Locations for DDB1 Gene
- chr11:61,299,451-61,342,596
- (GRCh38/hg38)
- Size:
- 43,146 bases
- Orientation:
- Minus strand
- chr11:61,066,919-61,110,068
- (GRCh37/hg19)
- Size:
- 43,150 bases
- Orientation:
- Minus strand
Genomic View for DDB1 Gene
Genes around DDB1 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 11q12.2 by HGNC
- 11q12.2 by Entrez Gene
- 11q12.2 by Ensembl
DDB1 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for DDB1 Gene
Proteins for DDB1 Gene
-
Protein details for DDB1 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- Q16531-DDB1_HUMAN
- Recommended name:
- DNA damage-binding protein 1
- Protein Accession:
- Q16531
- A6NG77
- B2R648
- B4DG00
- O15176
- Q13289
- Q58F96
Protein attributes for DDB1 Gene
- Size:
- 1140 amino acids
- Molecular mass:
- 126968 Da
- Quaternary structure:
-
- Component of the UV-DDB complex which includes DDB1 and DDB2; the heterodimer dimerizes to give rise to a heterotetramer when bound to damaged DNA (PubMed:9632823, PubMed:16223728, PubMed:16527807, PubMed:19109893, PubMed:22822215). The UV-DDB complex interacts with monoubiquitinated histone H2A and binds to XPC via the DDB2 subunit (PubMed:16473935). Component of numerous DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which consist of a core of DDB1, CUL4A or CUL4B and RBX1 (PubMed:11673459, PubMed:12732143, PubMed:15882621, PubMed:16678110, PubMed:18593899, PubMed:28886238, PubMed:28437394, PubMed:28302793, PubMed:31693891, PubMed:31686031, PubMed:31819272, PubMed:31693911). DDB1 may recruit specific substrate targeting subunits to the DCX complex (PubMed:11673459, PubMed:12732143, PubMed:15882621, PubMed:18593899, PubMed:28886238). These substrate targeting subunits are generally known as DCAF (DDB1- and CUL4-associated factor) or CDW (CUL4-DDB1-associated WD40-repeat) proteins (PubMed:17079684, PubMed:16949367, PubMed:18606781, PubMed:19608861, PubMed:16964240, PubMed:19966799). Interacts with AMBRA1, ATG16L1, BTRC, CRBN, DCAF1, DCAF4, DCAF5, DCAF6, DCAF7, DCAF8, DCAF9, DCAF10, DCAF11, DCAF12, DCAF15, DCAF16, DCAF17, DDA1, DET1, DTL, ERCC8, FBXW5, FBXW8, GRWD1, KATNB1, NLE1, NUP43, PAFAH1B1, PHIP, PWP1, RBBP4, RBBP5, RBBP7, COP1, SNRNP40, DCAF1, WDR5, WDR5B, WDR12, WDR26, WDR39, WDR42, WDR53, WDR59, WDR61, WSB1, WSB2, LRWD1 and WDTC1 (PubMed:14739464, PubMed:17079684, PubMed:16949367, PubMed:17041588, PubMed:18606781, PubMed:22935713, PubMed:23478445, PubMed:22118460, PubMed:25043012, PubMed:25108355). DCX complexes may associate with the COP9 signalosome, and this inhibits the E3 ubiquitin-protein ligase activity of the complex (PubMed:15448697, PubMed:16260596). Interacts with NF2, TSC1 and TSC2 (PubMed:18332868, PubMed:18381890). Interacts with AGO1 and AGO2 (PubMed:17932509). Associates with the E3 ligase complex containing DYRK2, EDD/UBR5, DDB1 and DCAF1 proteins (EDVP complex) (PubMed:19287380). Interacts directly with DYRK2 (PubMed:19287380). DCX(DTL) complex interacts with FBXO11; does not ubiquitinate and degradate FBXO11 (PubMed:19287380). Interacts with TRPC4AP (PubMed:19966799). Interacts with CRY1 and CRY2 (By similarity). The DDB1-CUL4A complex interacts with CRY1 (PubMed:26431207).
- (Microbial infection) Interacts with Simian virus 5 protein V.
- (Microbial infection) Interacts with hepatitis B virus protein HBX; the viral protein contains a short helical motif that competes for the same binding site as the N-terminal helical motif found in endogenous DCAF proteins.
Three dimensional structures from OCA and Proteopedia for DDB1 Gene
Protein Expression for DDB1 Gene
Post-translational modifications for DDB1 Gene
- Phosphorylated by ABL1.
- Ubiquitinated by CUL4A. Subsequently degraded by ubiquitin-dependent proteolysis.
- Acetylated, promoting interaction with CUL4 (CUL4A or CUL4B) and subsequent formation of DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes (PubMed:28886238). Deacetylation by SIRT7 impairs the interaction with CUL4 (CUL4A or CUL4B) and formation of DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes (PubMed:28886238).
-
Ubiquitination at Lys92, Lys823, Lys141, Lys153, Lys857, Lys191, Lys897, Lys917, Lys936, Lys298, Lys1067, Lys383, Lys1081, Lys408, Lys1121, Lys1131, Lys484, Lys570, Lys579, and Lys723
- NX_Q16531 (NX_Q16531-1)
- Modification sites at PhosphoSitePlus
Other Protein References for DDB1 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
- LifeSpan BioSciences DDB1 Antibody and DDB1 Monoclonal Antibody
- G Biosciences Immunotag™ DDB1 Antibody
- NSJ Bioreagents DDB1 Antibody
- Creative Diagnostics Anti-DDB1 monoclonal antibody, clone 5D6
- Novus Biologicals Antibodies for DDB1
-
Abcam antibodies for DDB1
- Invitrogen Antibodies for DDB1 (AFLGC-DDB1)
-
Santa Cruz Biotechnology (SCBT) Antibodies for DDB1
- Sino Biological Antibodies for DDB1
Protein Products
-
OriGene Purified Proteins for DDB1
- Search Origene for MassSpec and Protein Over-expression Lysates for DDB1
- Origene Custom Protein Services for DDB1
- Novus Biologicals proteins for DDB1
-
Abcam proteins for DDB1
Assay Products
- antibodies-online: Show 8 available DDB1 Elisa Kits ranked by validation data
- Compare Top DDB1 Elisa Kits
-
Quality Products:
No data available for DME Specific Peptides for DDB1 Gene
Domains & Families for DDB1 Gene
Gene Families for DDB1 Gene
- HGNC:
- Human Protein Atlas (HPA):
-
- Plasma proteins
- Predicted intracellular proteins
Protein Domains for DDB1 Gene
- InterPro:
- Blocks:
-
- CPSF A subunit C-terminal
- ProtoNet:
Suggested Antigen Peptide Sequences for DDB1 Gene
- GenScript: Design optimal peptide antigens:
-
- cDNA FLJ52436, highly similar to DNA damage-binding protein 1 (B4DG00_HUMAN)
- cDNA FLJ51165, highly similar to DNA damage-binding protein 1 (B4DZP5_HUMAN)
- Xeroderma pigmentosum group E-complementing protein (DDB1_HUMAN)
Graphical View of Domain Structure for InterPro Entry
Q16531UniProtKB/Swiss-Prot:
DDB1_HUMAN :- The core of the protein consists of three WD40 beta-propeller domains.
- Belongs to the DDB1 family.
- Domain:
-
- The core of the protein consists of three WD40 beta-propeller domains.
- Family:
-
- Belongs to the DDB1 family.
Function for DDB1 Gene
Molecular function for DDB1 Gene
- UniProtKB/Swiss-Prot Function:
- Protein, which is both involved in DNA repair and protein ubiquitination, as part of the UV-DDB complex and DCX (DDB1-CUL4-X-box) complexes, respectively (PubMed:15448697, PubMed:14739464, PubMed:16260596, PubMed:16482215, PubMed:17079684, PubMed:16407242, PubMed:16407252, PubMed:16940174). Core component of the UV-DDB complex (UV-damaged DNA-binding protein complex), a complex that recognizes UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair (PubMed:15448697, PubMed:16260596, PubMed:16407242, PubMed:16940174). The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches (PubMed:15448697, PubMed:16260596, PubMed:16407242, PubMed:16940174). Also functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins (PubMed:14739464, PubMed:16407252, PubMed:16482215, PubMed:17079684, PubMed:25043012, PubMed:25108355, PubMed:18332868, PubMed:18381890, PubMed:19966799, PubMed:22118460, PubMed:28886238). The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1 (PubMed:14739464, PubMed:16407252, PubMed:16482215, PubMed:17079684, PubMed:25043012, PubMed:25108355, PubMed:18332868, PubMed:18381890, PubMed:19966799, PubMed:22118460). DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage (PubMed:16678110, PubMed:17041588, PubMed:16473935, PubMed:18593899). The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair (PubMed:16678110, PubMed:17041588, PubMed:16473935, PubMed:18593899). DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER (PubMed:15882621). DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication (PubMed:17041588). DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR) (PubMed:12732143). The DDB1-CUL4A-DTL E3 ligase complex regulates the circadian clock function by mediating the ubiquitination and degradation of CRY1 (PubMed:26431207). DDB1-mediated CRY1 degradation promotes FOXO1 protein stability and FOXO1-mediated gluconeogenesis in the liver (By similarity).
- GENATLAS Biochemistry:
- damage specific DNA binding protein 1,p127 subunit,absent from cell strains from a minority of individuals with XP-E,possibly involved in nucleotide excision repair
Phenotypes From GWAS Catalog for DDB1 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0003676 | nucleic acid binding | IEA | -- |
| GO:0003677 | DNA binding | TAS | 8798680 |
| GO:0003684 | contributes_to damaged DNA binding | IDA | 22334663 |
| GO:0005515 | protein binding | IEA,IPI | 9418871 |
| GO:0030674 | protein binding, bridging | IPI | 14739464 |
Phenotypes for DDB1 Gene
- MGI mutant phenotypes for DDB1:
- inferred from 2 alleles
- GenomeRNAi human phenotypes for DDB1:
-
- no effect
- Decreased viability
- Synthetic lethal with MLN4924 (a NAE inhibitor)
- Increased shRNA abundance (Z-score > 2)
- Increased gamma-H2AX phosphorylation
- Increased endosome-nucleus distance (endosomes dispersed in the cell periphery)
- Decreased nuclei size in G2M
- Decreased viability of wild-type and TP53 knockout cells, decreased TP53 protein expression ratio (wild-type / TP53 knockout cells)
- Decreased number of cells in monopolar arrest with EMD534085 (a Kinesin-5 inhibitor)
- Negative genetic interaction between MUS81-/- and MUS81+/+
- Decreased homologous recombination repair frequency
- Decreased viability in ovarian lineage
- Negative genetic interaction between PTTG1-/- and PTTG1+/+
- Decreased shRNA abundance (Z-score < -2)
- S arrest
- Increased G1 length
- Decreased cell number, increased G2M DNA content
- Increased circadian rhythm amplitude
- Increased S length, increased G2 length
- Increased telomere dysfunction-induced foci (TIF) formation
Animal Models for DDB1 Gene
- MGI Knock Outs for DDB1:
-
- Ddb1 Ddb1<tm1.1Spg>
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
CRISPR Products
- Applied Biological Materials (abm): CRISPR Clones for DDB1 - Select products 50% OFF >
- * DDB1 CRISPR as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
-
OriGene CRISPR knockouts for DDB1
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for DDB1
-
Santa Cruz Biotechnology (SCBT) CRISPR for DDB1
miRNA for DDB1 Gene
- miRTarBase miRNAs that target DDB1
-
- hsa-miR-193b-3p (MIRT016411)
- hsa-miR-941 (MIRT036583)
- hsa-miR-186-5p (MIRT045270)
- hsa-miR-149-5p (MIRT045485)
- hsa-miR-30c-5p (MIRT047942)
- hsa-miR-26a-5p (MIRT050184)
- hsa-miR-3200-3p (MIRT052820)
- hsa-miR-493-3p (MIRT489974)
- hsa-miR-4330 (MIRT489975)
- hsa-miR-1304-3p (MIRT489976)
- hsa-miR-4257 (MIRT489977)
- hsa-miR-6847-5p (MIRT489978)
- hsa-miR-6876-5p (MIRT489979)
- hsa-miR-5197-3p (MIRT489980)
- hsa-miR-4476 (MIRT489981)
- hsa-miR-559 (MIRT489982)
- hsa-miR-548y (MIRT489983)
- hsa-miR-548w (MIRT489984)
- hsa-miR-548o-5p (MIRT489985)
- hsa-miR-548j-5p (MIRT489986)
- hsa-miR-548i (MIRT489987)
- hsa-miR-548h-5p (MIRT489988)
- hsa-miR-548d-5p (MIRT489989)
- hsa-miR-548c-5p (MIRT489990)
- hsa-miR-548bb-5p (MIRT489991)
- hsa-miR-548b-5p (MIRT489992)
- hsa-miR-548ay-5p (MIRT489993)
- hsa-miR-548au-5p (MIRT489994)
- hsa-miR-548as-5p (MIRT489995)
- hsa-miR-548ar-5p (MIRT489996)
- hsa-miR-548aq-5p (MIRT489997)
- hsa-miR-548ap-5p (MIRT489998)
- hsa-miR-548am-5p (MIRT489999)
- hsa-miR-548ak (MIRT490000)
- hsa-miR-548ae-5p (MIRT490001)
- hsa-miR-548ad-5p (MIRT490002)
- hsa-miR-548ab (MIRT490003)
- hsa-miR-548a-5p (MIRT490004)
- hsa-miR-548n (MIRT490005)
- hsa-miR-3941 (MIRT611530)
- hsa-miR-7162-5p (MIRT611531)
- hsa-miR-516b-3p (MIRT611532)
- hsa-miR-516a-3p (MIRT611533)
- hsa-miR-4789-3p (MIRT611534)
- hsa-miR-603 (MIRT611535)
- hsa-miR-362-3p (MIRT611536)
- hsa-miR-329-3p (MIRT611537)
- hsa-miR-8485 (MIRT611538)
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for DDB1
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Clone Products
- Applied Biological Materials (abm): Clones for DDB1 - Select products 50% OFF >
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- Sino Biological Human cDNA Clone for DDB1
- Addgene plasmids for DDB1
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for DDB1
No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for DDB1 Gene
Localization for DDB1 Gene
Subcellular locations from UniProtKB/Swiss-Prot for DDB1 Gene
- Cytoplasm. Nucleus. Note=Primarily cytoplasmic (PubMed:10777491, PubMed:11673459). Translocates to the nucleus following UV irradiation and subsequently accumulates at sites of DNA damage (PubMed:10777491, PubMed:11673459). {ECO:0000269 PubMed:10777491, ECO:0000269 PubMed:11673459}.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| extracellular | 4 |
| cytosol | 4 |
| mitochondrion | 3 |
| plasma membrane | 2 |
| cytoskeleton | 2 |
| peroxisome | 1 |
| endoplasmic reticulum | 1 |
| endosome | 1 |
| lysosome | 1 |
| golgi apparatus | 1 |
- Nucleoplasm (4)
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000784 | nuclear chromosome, telomeric region | HDA | 19135898 |
| GO:0005615 | extracellular space | HDA | 22664934 |
| GO:0005634 | nucleus | IEA,IDA | 18593899 |
| GO:0005654 | nucleoplasm | TAS | -- |
| GO:0005737 | cytoplasm | IEA,IDA | 18593899 |
Pathways & Interactions for DDB1 Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | Transcription-Coupled Nucleotide Excision Repair (TC-NER) | ||
| 2 | Nucleotide excision repair | ||
| 3 | DNA Damage | ||
| 4 | Toll-like Receptor Signaling Pathway |
.37
|
|
| 5 | Human cytomegalovirus infection | ||
Pathways by source for DDB1 Gene
12 Reactome pathways for DDB1 Gene
5 KEGG pathways for DDB1 Gene
1 Cell Signaling Technology pathway for DDB1 Gene
UniProtKB/Swiss-Prot Q16531-DDB1_HUMAN
- Pathway: Protein modification; protein ubiquitination.
Interacting Proteins for DDB1 Gene
Selected Interacting proteins:
Q16531-DDB1_HUMAN
ENSP00000301764
for DDB1 Gene via
UniProtKB
MINT
STRING
IID
GPS-Prot Interaction Network for DDB1
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000715 | nucleotide-excision repair, DNA damage recognition | TAS | -- |
| GO:0000717 | nucleotide-excision repair, DNA duplex unwinding | TAS | -- |
| GO:0006281 | DNA repair | IEA,TAS | 8798680 |
| GO:0006283 | transcription-coupled nucleotide-excision repair | TAS | -- |
| GO:0006289 | nucleotide-excision repair | TAS,IBA | 21873635 |
Transcripts for DDB1 Gene
mRNA/cDNA for DDB1 Gene
- 1 REFSEQ mRNAs :
- 20 NCBI additional mRNA sequence :
- 25 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
-
- ENST00000301764 4245 nts (view in UCSC)
- ENST00000451943 1224 nts (view in UCSC)
- ENST00000545894 2282 nts (view in UCSC)
- ENST00000540166 3906 nts (view in UCSC)
- ENST00000538470 858 nts (view in UCSC)
CRISPR Products
- Applied Biological Materials (abm): CRISPR Clones for DDB1 - Select products 50% OFF >
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-
OriGene CRISPR knockouts for DDB1
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for DDB1
-
Santa Cruz Biotechnology (SCBT) CRISPR for DDB1
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for DDB1
- Browse OriGene Inhibitory RNA Products For DDB1
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DDB1
Clone Products
- Applied Biological Materials (abm): Clones for DDB1 - Select products 50% OFF >
- * DDB1 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Sino Biological Human cDNA Clone for DDB1
- Addgene plasmids for DDB1
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for DDB1
| ExUns: | 1 | ^ | 2a | · | 2b | ^ | 3 | ^ | 4 | ^ | 5a | · | 5b | ^ | 6 | ^ | 7a | · | 7b | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 | ^ | 12 | ^ | 13 | ^ | 14 | ^ | 15 | ^ | 16 | ^ | 17 | ^ | 18a | · | 18b | ^ | 19 | ^ | 20 | ^ | 21 | ^ | 22 | ^ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SP1: | - | - | ||||||||||||||||||||||||||||||||||||||||||||||||||
| SP2: | - | |||||||||||||||||||||||||||||||||||||||||||||||||||
| SP3: | - | - | - | - | - | |||||||||||||||||||||||||||||||||||||||||||||||
| SP4: | - | - | - | |||||||||||||||||||||||||||||||||||||||||||||||||
| SP5: | - | - | - | - | ||||||||||||||||||||||||||||||||||||||||||||||||
| SP6: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| SP7: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| SP8: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| SP9: |
| ExUns: | 23 | ^ | 24 | ^ | 25a | · | 25b | ^ | 26a | · | 26b | · | 26c | · | 26d | ^ | 27a | · | 27b | · | 27c | · | 27d | · | 27e | ^ | 28 | ^ | 29a | · | 29b |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SP1: | - | - | |||||||||||||||||||||||||||||
| SP2: | |||||||||||||||||||||||||||||||
| SP3: | - | - | - | - | - | - | |||||||||||||||||||||||||
| SP4: | |||||||||||||||||||||||||||||||
| SP5: | |||||||||||||||||||||||||||||||
| SP6: | - | - | - | ||||||||||||||||||||||||||||
| SP7: | - | ||||||||||||||||||||||||||||||
| SP8: | |||||||||||||||||||||||||||||||
| SP9: |
Relevant External Links for DDB1 Gene
- GeneLoc Exon Structure for
- DDB1
Expression for DDB1 Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
-
Heart (Cardiovascular System)
- Atrioventricular Canal Cells Atrioventricular Canal
- Outflow Tract
- Brain (Nervous System)
- Intestine (Gastrointestinal Tract)
- Bone (Muscoskeletal System)
-
Uterus (Reproductive System)
-
Colon (Gastrointestinal Tract)
-
Prostate (Endocrine System)
-
Placenta (Extraembryonic Tissues)
-
Thyroid (Endocrine System)
-
Kidney (Urinary System)
-
Testis (Reproductive System)
-
Adrenal Gland (Endocrine System)
-
Ovary (Reproductive System)
This gene is overexpressed in Lymph node (6.9).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for DDB1 Gene
- Elite partner
Transcriptomic regulation report from SPP (The Signaling Pathways Project) for DDB1
SOURCE GeneReport for Unigene cluster for DDB1 Gene:
Hs.290758Evidence on tissue expression from TISSUES for DDB1 Gene
- Nervous system(5)
- Lung(4.9)
- Skin(4.8)
- Liver(4.7)
- Blood(4.6)
- Eye(4.3)
- Intestine(4.2)
- Kidney(3.7)
- Heart(3.2)
- Muscle(2.9)
- Adrenal gland(2.7)
- Pancreas(2.7)
- Lymph node(2.6)
- Spleen(2.5)
- Bone marrow(2.5)
- Thyroid gland(2.4)
- Stomach(2.3)
Phenotype-based relationships between genes and organs from Gene ORGANizer for DDB1 Gene
Germ Layers:
- ectoderm
Systems:
- integumentary
Regions:
General:
- skin
Primer Products
-
OriGene qPCR primer pairs for DDB1
-
OriGene qPCR primer pairs and template standards for DDB1
Gene Expression Assay Products
No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for DDB1 Gene
Orthologs for DDB1 Gene
This gene was present in the common ancestor of eukaryotes.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| Chimpanzee (Pan troglodytes) |
Mammalia | DDB1 30 31 |
|
OneToOne | |
| Platypus (Ornithorhynchus anatinus) |
Mammalia | DDB1 31 |
|
OneToOne | |
| Dog (Canis familiaris) |
Mammalia | DDB1 30 31 |
|
OneToOne | |
| Cow (Bos Taurus) |
Mammalia | DDB1 30 31 |
|
OneToOne | |
| Mouse (Mus musculus) |
Mammalia | Ddb1 30 17 31 |
|
OneToOne | |
| Rat (Rattus norvegicus) |
Mammalia | Ddb1 30 |
|
||
| Oppossum (Monodelphis domestica) |
Mammalia | DDB1 31 |
|
OneToOne | |
| Chicken (Gallus gallus) |
Aves | DDB1 30 31 |
|
OneToOne | |
| Lizard (Anolis carolinensis) |
Reptilia | DDB1 31 |
|
OneToOne | |
| Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | ddb1 30 |
|
||
| Str.4452 30 |
|
||||
| African clawed frog (Xenopus laevis) |
Amphibia | MGC68476 30 |
|
||
| Zebrafish (Danio rerio) |
Actinopterygii | ddb1 30 31 31 |
|
OneToMany | |
| zgc63840 30 |
|
||||
| Rainbow Trout (Oncorhynchus mykiss) |
Actinopterygii | Omy.752 30 |
|
||
| African malaria mosquito (Anopheles gambiae) |
Insecta | AgaP_AGAP002472 30 |
|
||
| Fruit Fly (Drosophila melanogaster) |
Insecta | pic 30 31 |
|
OneToOne | |
| DDB1 32 |
|
|
|||
| Worm (Caenorhabditis elegans) |
Secernentea | ddb-1 31 |
|
OneToOne | |
| M18.5 32 |
|
|
|||
| Baker's yeast (Saccharomyces cerevisiae) |
Saccharomycetes | RSE1 31 |
|
OneToMany | |
| Thale Cress (Arabidopsis thaliana) |
eudicotyledons | DDB1A 30 |
|
||
| Rice (Oryza sativa) |
Liliopsida | Os05g0592400 30 |
|
||
| Os.419 30 |
|
||||
| Barley (Hordeum vulgare) |
Liliopsida | Hv.5462 30 |
|
||
| Wheat (Triticum aestivum) |
Liliopsida | Ta.14606 30 |
|
||
| Sea Squirt (Ciona savignyi) |
Ascidiacea | -- 31 |
|
OneToOne | |
| Sea Vase (Ciona intestinalis) |
Ascidiacea | Cin.8274 30 |
|
- Species where no ortholog for DDB1 was found in the sources mined by GeneCards:
-
- A. gosspyii yeast (Eremothecium gossypii)
- Actinobacteria (Mycobacterium tuberculosis)
- Alicante grape (Vitis vinifera)
- Alpha proteobacteria (Wolbachia pipientis)
- Amoeba (Dictyostelium discoideum)
- Archea (Pyrococcus horikoshii)
- Beta proteobacteria (Neisseria meningitidis)
- Bread mold (Neurospora crassa)
- Chromalveolata (Phytophthora infestans)
- Common water flea (Daphnia pulex)
- Corn (Zea mays)
- E. coli (Escherichia coli)
- Filamentous fungi (Aspergillus nidulans)
- Firmicute Bacteria (Streptococcus pneumoniae)
- Fission Yeast (Schizosaccharomyces pombe)
- Green Algae (Chlamydomonas reinhardtii)
- Honey Bee (Apis mellifera)
- K. Lactis Yeast (Kluyveromyces lactis)
- Loblloly Pine (Pinus taeda)
- Malaria Parasite (Plasmodium falciparum)
- Medicago Trunc (Medicago Truncatula)
- Moss (Physcomitrella patens)
- Orangutan (Pongo pygmaeus)
- Pig (Sus scrofa)
- Rice Blast Fungus (Magnaporthe grisea)
- Schistosome Parasite (Schistosoma mansoni)
- Sea Anemone (Nematostella vectensis)
- Sea Urchin (Strongylocentrotus purpuratus)
- Sorghum (Sorghum bicolor)
- Soybean (Glycine max)
- Stem Rust Fungus (Puccinia graminis)
- Sugarcane (Saccharum officinarum)
- Tomato (Lycopersicon esculentum)
- Toxoplasmosis (Toxoplasma gondii)
- Trichoplax (Trichoplax adhaerens)
Evolution for DDB1 Gene
- ENSEMBL:
- Gene Tree for DDB1 (if available)
- TreeFam:
- Gene Tree for DDB1 (if available)
- Aminode:
- Evolutionary constrained regions (ECRs) for DDB1: view image
Paralogs for DDB1 Gene
Variants for DDB1 Gene
Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for DDB1 Gene
| SNP ID | Clinical significance and condition | Chr 11 pos | Variation | AA Info | Type |
|---|---|---|---|---|---|
| 718554 | Benign: not provided | 61,325,604(-) | C/T | INTRON_VARIANT | |
| 776617 | Benign: not provided | 61,310,416(-) | A/G | SYNONYMOUS_VARIANT | |
| 782214 | Benign: not provided | 61,322,299(-) | C/T | SYNONYMOUS_VARIANT | |
| 790094 | Benign: not provided | 61,309,037(-) | G/A | SYNONYMOUS_VARIANT | |
| 816932 | Uncertain Significance: Abnormal heart morphology | 61,316,553(-) | G/A | MISSENSE_VARIANT |
Residual Variation Intolerance Score:
1.33% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
0.70;
14.87% of all genes are more intolerant (likely to be disease-causing)
Additional Variant Information for DDB1 Gene
- SNPedia medical, phenotypic, and genealogical associations of SNPs for
- DDB1
SNP Genotyping and Copy Number Assay Products
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDB1 Gene
Disorders for DDB1 Gene
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| xeroderma pigmentosum, complementation group e |
|
|
| xeroderma pigmentosum group e |
|
|
| hepatitis b |
|
|
| vitelliform macular dystrophy |
|
|
| xeroderma pigmentosum, variant type |
|
Search DDB1 in MalaCards
View complete list of genes associated with diseases
Additional Disease Information for DDB1
No data available for UniProtKB/Swiss-Prot and Genatlas for DDB1 Gene
Publications for DDB1 Gene
- Protein kinase DYRK2 is a scaffold that facilitates assembly of an E3 ligase. (PMID: 19287380) Maddika S … Chen J (Nature cell biology 2009) 3 4 23
- WD40 protein FBW5 promotes ubiquitination of tumor suppressor TSC2 by DDB1-CUL4-ROC1 ligase. (PMID: 18381890) Hu J … Xiong Y (Genes & development 2008) 3 4 23
- Human immunodeficiency virus type 1 Vpr-binding protein VprBP, a WD40 protein associated with the DDB1-CUL4 E3 ubiquitin ligase, is essential for DNA replication and embryonic development. (PMID: 18606781) McCall CM … Xiong Y (Molecular and cellular biology 2008) 3 4 23
- The cullin 4B-based UV-damaged DNA-binding protein ligase binds to UV-damaged chromatin and ubiquitinates histone H2A. (PMID: 18593899) Guerrero-Santoro J … Rapić-Otrin V (Cancer research 2008) 3 4 23
- CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. (PMID: 17041588) Higa LA … Zhang H (Nature cell biology 2006) 3 4 23
ExternalLinks
Products for DDB1 Gene
- Custom Antibody ServicesOriGene Antibodies for DDB1
- Browse OriGene ELISA Kits
- Custom Assay Services
- OriGene Purified Proteins for DDB1
- Search Origene for MassSpec and Protein Over-expression Lysates for DDB1
- Origene Custom Protein Services for DDB1
- Origene shrna, sirna, and RNAi products in human, mouse, rat for DDB1
- Browse OriGene Inhibitory RNA Products For DDB1
- OriGene qPCR primer pairs for DDB1
- OriGene qPCR primer pairs and template standards for DDB1
- OriGene CRISPR knockouts for DDB1
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Browse OriGene miRNA Products For DDB1
- Sino Biological Human cDNA Clone for DDB1
- Browse Sino Biological Recombinant Proteins
- Browse Sino Biological Cell Lysates
- Sino Biological Antibodies for DDB1
- Browse Sino Biological Assays
- Browse Antibodies
- Browse cDNA Clones
- Browse ELISA Kits
- Browse CRO Services
- High-throughput Antibody Production Service
- Protein Production Service
- Epitope Tag Antibodies & Reporter Protein Antibodies
- Lentiviral ORF Clones
- Novus Biologicals Antibodies for DDB1
- Novus Biologicals proteins for DDB1
- Browse Antibodies
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- Abcam antibodies for DDB1
- Abcam proteins for DDB1
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- Browse Primary Antibodies
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- Invitrogen Antibodies for DDB1 (AFLGC-DDB1)
- VectorBuilder Custom and pre-made DNA vectors for DDB1 (ie. gene expression, shRNA knockdown, CRISPR)
- VectorBuilder Viral vectors for DDB1 (ie. lentivirus, AAV, adenovirus)
- VectorBuilder CRISPR vectors for DDB1 (ie. knockout, knockin, CRISPRa, CRISPRi)
- VectorBuilder Virus packaging for DDB1 CRISPR vectors (ie. lentivirus, AAV, adenovirus)
- VectorBuilder Stable cell line generation for DDB1
- Addgene plasmids for DDB1
- antibodies-online: Show 186 available DDB1 Antibodies ranked by validation data
- Compare Top DDB1 Antibodies
- antibodies-online: Show 8 available DDB1 Elisa Kits ranked by validation data
- Compare Top DDB1 Elisa Kits
- Quality Products:
- antibodies-online: Show 4 available DDB1 Proteins ranked by validation data
- Compare Top DDB1 Proteins
- Santa Cruz Biotechnology (SCBT) Antibodies for DDB1
- Search Santa Cruz Biotechnology (SCBT) for DDB1 siRNA/shRNA
- Santa Cruz Biotechnology (SCBT) CRISPR for DDB1
- Browse GeneCopoeia Cell Lines
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for DDB1
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for DDB1
- Search GeneCopoeia for miRNA 3'UTR Target clone products for DDB1
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DDB1
Sources for DDB1 Gene
- (1) GeneCards
- (2) HGNC
- (3) NCBI Entrez Gene
- (4) UniProtKB/Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) Cell Signaling Technology
- (12) GO
- (13) UniProtKB/TrEMBL
- (14) InterPro
- (15) ProtoNet
- (16) Blocks
- (17) MGI
- (18) IUBMB
- (19) KEGG
- (20) MINT
- (21) STRING
- (22) IntAct
- (23) Novoseek
- (24) PharmGKB
- (25) DrugBank
- (26) HMDB
- (27) ASD
- (28) SAGE
- (29) SOURCE
- (30) HomoloGene
- (31) PanEnsembl
- (32) euGenes
- (33) SGD
- (34) FlyBase
- (35) WormBase
- (36) Pseudogene
- (37) DGV
- (38) dbSNP
- (39) GenAtlas
- (40) HGMD
- (41) GAD
- (42) BGMUT
- (43) HuGE
- (44) Atlas
- (45) GenBank
- (46) HORDE
- (47) HUGE
- (48) IMGT
- (49) Leiden
- (50) miRBase
- (51) DME
- (52) OriGene
- (53) PubMed
- (54) R&D Systems
- (55) TGDB
- (56) Tocris
- (57) Abcam
- (58) Novus Biologicals
- (59) ProSpec
- (60) Sino Biological
- (61) GenScript
- (62) Qiagen
- (63) OCA
- (64) Proteopedia
- (65) MOPED
- (66) neXtProt
- (67) Reactome
- (68) GeneGo (Thomson Reuters)
- (69) DISEASES
- (70) SIMAP
- (71) GenomeRNAi
- (72) LifeMap
- (73) miRTarBase
- (74) MalaCards
- (75) Invitrogen
- (76) BitterDB
- (77) ESI-BIO
- (78) RefSeq
- (79) BioSystems
- (80) MaxQB
- (81) IUPHAR
- (82) BioGPS
- (83) Illumina
- (84) COMPARTMENTS
- (85) HOMER
- (86) PaxDb
- (87) ApexBio
- (88) Addgene
- (89) antibodies-online
- (90) CYP
- (91) NONCODE
- (92) TreeFam
- (93) PathCards
- (94) GeneReviews
- (95) GeneTex
- (96) Taconic Biosciences
- (97) GTEx
- (98) ProteomicsDB
- (99) SCBT
- (100) DGIdb
- (101) ClinicalTrials
- (102) RVIS
- (103) SIGNOR
- (104) diseasecard
- (105) NIH Rare Diseases
- (106) Orphanet
- (107) UMLS
- (108) GTR
- (109) Disease Ontology
- (110) Genetics Home Reference
- (111) MeSH
- (112) MedlinePlus
- (113) CDC
- (114) NINDS
- (115) NCBI Bookshelf
- (116) ClinVar
- (117) Gene Damage Index
- (118) HPO
- (119) UDN
- (120) VISTA
- (121) FANTOM5
- (122) ENCODE
- (123) ProSci
- (124) Horizon
- (125) The Signaling Pathways Project (SPP)
- (126) IID
- (127) VectorBuilder
- (128) SNPedia
- (129) BRCA Exchange
- (130) CIViC
- (131) ProteoGenix
- (132) dbSUPER
- (133) TISSUES
- (134) Gene ORGANizer
- (135) abm
- (136) Human Protein Atlas
- (137) GWAS Catalog
- (138) Monarch Initiative
- (139) DataMed
- (140) HumanCyc
- (141) UCNEbase
- (142) EPDnew
- (143) Applied Biosystems
- (144) GlyConnect
- (145) Aminode
- (146) GeneCopoeia
- (147) GPS-Prot
- (148) RNACentral
- (149) LncRNADisease
- (150) LOVD
- (151) miR2Disease
- (152) DiseaseEnhancer
- (153) Boster Bio
- (154) Biorbyt
- (155) Biocompare
- (156) Mastermind
- (157) CTD^2 Dashboard
- (158) CraniofacialAtlas
- (159) GeneImprint
- (160) Synthego
- (161) ENA
- (162) GtRNAdb
- (163) LncBase
- (164) LncBook
- (165) LNCipedia
- (166) Modomics
- (167) PDBe
- (168) Rfam
- (169) SILVA
- (170) snOPY
- (171) SRPDB
- (172) GENCODE
- (173) TarBase
- (174) Signalway Antibody
- (175) Open Targets Platform
- (176) 5SRRNADB
- (177) snoDB
- (178) MirGeneDB