Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SLX4 (SLX4 structure-specific endonuclease subunit)

Identity

Other namesBTBD12
FANCP
MUS312
HGNC (Hugo) SLX4
LocusID (NCBI) 84464
Atlas_Id 51673
Location 16p13.3
Location_base_pair Starts at 3631184 and ends at 3661585 bp from pter ( according to hg19-Feb_2009)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Solid tumors implicated (Data extracted from papers in the Atlas)
  Lung: Translocations in Small Cell Carcinoma

Other Cancer prone implicated (Data extracted from papers in the Atlas)
  Fanconi anaemia

External links

Nomenclature
HGNC (Hugo)SLX4   23845
Cards
Entrez_Gene (NCBI)SLX4  84464  SLX4 structure-specific endonuclease subunit
GeneCards (Weizmann)SLX4
Ensembl hg19 (Hinxton)ENSG00000188827 [Gene_View]  chr16:3631184-3661585 [Contig_View]  SLX4 [Vega]
Ensembl hg38 (Hinxton)ENSG00000188827 [Gene_View]  chr16:3631184-3661585 [Contig_View]  SLX4 [Vega]
ICGC DataPortalENSG00000188827
TCGA cBioPortalSLX4
AceView (NCBI)SLX4
Genatlas (Paris)SLX4
WikiGenes84464
SOURCE (Princeton)SLX4
Genomic and cartography
GoldenPath hg19 (UCSC)SLX4  -     chr16:3631184-3661585 -  16p13.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SLX4  -     16p13.3   [Description]    (hg38-Dec_2013)
EnsemblSLX4 - 16p13.3 [CytoView hg19]  SLX4 - 16p13.3 [CytoView hg38]
Mapping of homologs : NCBISLX4 [Mapview hg19]  SLX4 [Mapview hg38]
OMIM189960   613278   613951   
Gene and transcription
Genbank (Entrez)AB058687 AB075867 AK095411 AK122775 AL442083
RefSeq transcript (Entrez)NM_032444
RefSeq genomic (Entrez)NC_000016 NC_018927 NG_028123 NT_010393 NW_004929400
Consensus coding sequences : CCDS (NCBI)SLX4
Cluster EST : UnigeneHs.143681 [ NCBI ]
CGAP (NCI)Hs.143681
Alternative Splicing : Fast-db (Paris)GSHG0033882
Alternative Splicing GalleryENSG00000188827
Gene ExpressionSLX4 [ NCBI-GEO ]     SLX4 [ SEEK ]   SLX4 [ MEM ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
BioGPS (Tissue expression)84464
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8IY92 (Uniprot)
NextProtQ8IY92  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8IY92
Splice isoforms : SwissVarQ8IY92 (Swissvar)
PhosPhoSitePlusQ8IY92
Domaine pattern : Prosite (Expaxy)BTB (PS50097)   
Domains : Interpro (EBI)BTB/POZ-like    BTB/POZ_fold    BTB_POZ    Structure-sp_endonuc_su_Slx4   
Domain families : Pfam (Sanger)BTB (PF00651)    Slx4 (PF09494)   
Domain families : Pfam (NCBI)pfam00651    pfam09494   
Domain families : Smart (EMBL)BTB (SM00225)  
DMDM Disease mutations84464
Blocks (Seattle)SLX4
PDB (SRS)4M7C    4UYI   
PDB (PDBSum)4M7C    4UYI   
PDB (IMB)4M7C    4UYI   
PDB (RSDB)4M7C    4UYI   
Structural Biology KnowledgeBase4M7C    4UYI   
SCOP (Structural Classification of Proteins)4M7C    4UYI   
CATH (Classification of proteins structures)4M7C    4UYI   
Human Protein AtlasENSG00000188827
Peptide AtlasQ8IY92
HPRD12537
IPIIPI00291796   IPI00412364   
Protein Interaction databases
DIP (DOE-UCLA)Q8IY92
IntAct (EBI)Q8IY92
FunCoupENSG00000188827
BioGRIDSLX4
IntegromeDBSLX4
STRING (EMBL)SLX4
ZODIACSLX4
Ontologies - Pathways
QuickGOQ8IY92
Ontology : AmiGOdouble-strand break repair via homologous recombination  double-strand break repair via homologous recombination  nuclear chromosome, telomeric region  nuclear chromatin  protein binding  nucleoplasm  nucleoplasm  cytoplasm  DNA replication  DNA repair  DNA repair  nucleotide-excision repair  double-strand break repair  enzyme activator activity  crossover junction endodeoxyribonuclease activity  DNA double-strand break processing involved in repair via single-strand annealing  5'-flap endonuclease activity  cell junction  Slx1-Slx4 complex  interstrand cross-link repair  positive regulation of catalytic activity  3'-flap endonuclease activity  Holliday junction resolvase complex  ERCC4-ERCC1 complex  response to intra-S DNA damage checkpoint signaling  t-circle formation  positive regulation of t-circle formation  
Ontology : EGO-EBIdouble-strand break repair via homologous recombination  double-strand break repair via homologous recombination  nuclear chromosome, telomeric region  nuclear chromatin  protein binding  nucleoplasm  nucleoplasm  cytoplasm  DNA replication  DNA repair  DNA repair  nucleotide-excision repair  double-strand break repair  enzyme activator activity  crossover junction endodeoxyribonuclease activity  DNA double-strand break processing involved in repair via single-strand annealing  5'-flap endonuclease activity  cell junction  Slx1-Slx4 complex  interstrand cross-link repair  positive regulation of catalytic activity  3'-flap endonuclease activity  Holliday junction resolvase complex  ERCC4-ERCC1 complex  response to intra-S DNA damage checkpoint signaling  t-circle formation  positive regulation of t-circle formation  
Pathways : KEGGFanconi anemia pathway   
Protein Interaction DatabaseSLX4
Atlas of Cancer Signalling NetworkSLX4
Wikipedia pathwaysSLX4
Orthology - Evolution
OrthoDB84464
GeneTree (enSembl)ENSG00000188827
Phylogenetic Trees/Animal Genes : TreeFamSLX4
Homologs : HomoloGeneSLX4
Homology/Alignments : Family Browser (UCSC)SLX4
Gene fusions - Rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerSLX4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SLX4
dbVarSLX4
ClinVarSLX4
1000_GenomesSLX4 
Exome Variant ServerSLX4
Exome Aggregation Consortium (ExAC)ENSG00000188827
SNP (GeneSNP Utah)SLX4
SNP : HGBaseSLX4
Genetic variants : HAPMAPSLX4
Genomic Variants (DGV)SLX4 [DGVbeta]
Mutations
ICGC Data PortalSLX4 
TCGA Data PortalSLX4 
Tumor PortalSLX4
TCGA Copy Number PortalSLX4
Somatic Mutations in Cancer : COSMICSLX4 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
BioMutasearch SLX4
DgiDB (Drug Gene Interaction Database)SLX4
DoCM (Curated mutations)SLX4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SLX4 (select a term)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)16:3631184-3661585
CONAN: Copy Number AnalysisSLX4 
Mutations and Diseases : HGMDSLX4
OMIM189960    613278    613951   
MedgenSLX4
NextProtQ8IY92 [Medical]
TSGene84464
GENETestsSLX4
Huge Navigator SLX4 [HugePedia]  SLX4 [HugeCancerGEM]
snp3D : Map Gene to Disease84464
BioCentury BCIQSLX4
General knowledge
Chemical/Protein Interactions : CTD84464
Chemical/Pharm GKB GenePA134983583
Clinical trialSLX4
Other databases
Probes
Litterature
PubMed46 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSLX4
GoPubMedSLX4
iHOPSLX4
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Jan 16 19:31:30 CET 2016

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