This gene encodes a protein that is an important regulator of genome stability. The protein represents the catalytic subunit of the SLX1-SLX4 structure-specific endonuclease, which can resolve DNA secondary structures that are formed during repair and recombination processes. Two identical copies of this gene are located on the p arm of chromosome 16 due to a segmental duplicat... See more...

Aliases for SLX1A Gene

Aliases for SLX1A Gene

  • SLX1 Homolog A, Structure-Specific Endonuclease Subunit 2 3 5
  • Structure-Specific Endonuclease Subunit SLX1 3 4
  • GIY-YIG Domain-Containing Protein 1 3 4
  • GIYD1 3 4
  • SLX1 Structure-Specific Endonuclease Subunit Homolog A (S. Cerevisiae) 2
  • SLX1 Structure-Specific Endonuclease Subunit Homolog A 3
  • GIY-YIG Domain Containing 1 2
  • EC 3.1.-.- 4
  • SLX1A 5
  • GIYD2 4
  • SLX1 4

External Ids for SLX1A Gene

Previous HGNC Symbols for SLX1A Gene

  • GIYD1

Previous GeneCards Identifiers for SLX1A Gene

  • GC16P030208
  • GC16P030210
  • GC16P030215
  • GC16P030218
  • GC16P030196
  • GC16P030200
  • GC16P030276
  • GC16P030281
  • GC16P030195
  • GC16P030328
  • GC16P030222
  • GC16P030233
  • GC16P030242
  • GC16P030247
  • GC16P030252
  • GC16P030260
  • GC16P030265
  • GC16P030270
  • GC16P030376
  • GC16P030478

Summaries for SLX1A Gene

Entrez Gene Summary for SLX1A Gene

  • This gene encodes a protein that is an important regulator of genome stability. The protein represents the catalytic subunit of the SLX1-SLX4 structure-specific endonuclease, which can resolve DNA secondary structures that are formed during repair and recombination processes. Two identical copies of this gene are located on the p arm of chromosome 16 due to a segmental duplication; this record represents the more centromeric copy. Alternative splicing results in multiple transcript variants. Read-through transcription also occurs between this gene and the downstream SULT1A3 (sulfotransferase family, cytosolic, 1A, phenol-preferring, member 3) gene. [provided by RefSeq, Nov 2010]

GeneCards Summary for SLX1A Gene

SLX1A (SLX1 Homolog A, Structure-Specific Endonuclease Subunit) is a Protein Coding gene. Diseases associated with SLX1A include Interstitial Nephritis, Karyomegalic and Fanconi Anemia, Complementation Group P. Among its related pathways are DNA Double-Strand Break Repair and Resolution of D-loop Structures through Holliday Junction Intermediates. Gene Ontology (GO) annotations related to this gene include crossover junction endodeoxyribonuclease activity and 5'-flap endonuclease activity. An important paralog of this gene is SLX1B.

UniProtKB/Swiss-Prot Summary for SLX1A Gene

  • Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLX1A Gene

Genomics for SLX1A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SLX1A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J030192 Promoter/Enhancer 0.8 EPDnew Ensembl dbSUPER 250.7 0.0 -42 3.2 BOLA2B SLX1A SLX1A-SULT1A3 lnc-NPIPB13-1 BOLA2 CORO1A HSALNG0110697
GH16J029803 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 71 -383.1 -383101 14.9 BCLAF1 SP1 ZNF207 NCOR1 MYC ZNF654 ZNF600 IKZF1 SIX5 SSRP1 PRRT2 ENSG00000280893 LOC112268170 MAZ piR-45320 piR-53734 piR-50884 piR-51020 PAGR1 SRCAP
GH16J030195 Promoter/Enhancer 0.5 Ensembl dbSUPER 250.7 +2.0 1958 0.4 BOLA2B SLX1A SLX1A-SULT1A3 SULT1A3 HSALNG0110697
GH16J030956 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 44.4 +764.0 764048 3.4 BCLAF1 SP1 ZNF207 IKZF1 MYC ZNF600 SSRP1 ZNF580 ZMYM3 ATF2 SETD1A ENSG00000275263 SRCAP INO80E ENSG00000260267 ZNF764 SMG1P5 ENSG00000260304 ZNF747 RNF40
GH16J030566 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 31.6 +376.1 376091 6.1 BCLAF1 SP1 ZNF207 IKZF1 ZNF654 ZNF600 SIX5 ZNF580 ZNF592 ATF2 ZNF688 lnc-ITGAL-5 lnc-ITGAL-6 lnc-ZNF785-2 SETD1A SRCAP ENSG00000260267 ZNF747 NPIPB13 INO80E
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLX1A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLX1A

Genomic Locations for SLX1A Gene

Latest Assembly
chr16:30,193,843-30,197,566
(GRCh38/hg38)
Size:
3,724 bases
Orientation:
Plus strand

Previous Assembly
chr16:30,205,164-30,208,887
(GRCh37/hg19 by Entrez Gene)
Size:
3,724 bases
Orientation:
Plus strand

chr16:30,205,208-30,208,882
(GRCh37/hg19 by Ensembl)
Size:
3,675 bases
Orientation:
Plus strand

Genomic View for SLX1A Gene

Genes around SLX1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLX1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLX1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLX1A Gene

Proteins for SLX1A Gene

  • Protein details for SLX1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BQ83-SLX1_HUMAN
    Recommended name:
    Structure-specific endonuclease subunit SLX1
    Protein Accession:
    Q9BQ83
    Secondary Accessions:
    • B7ZME1
    • Q6NTG6

    Protein attributes for SLX1A Gene

    Size:
    275 amino acids
    Molecular mass:
    30771 Da
    Cofactor:
    Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
    Quaternary structure:
    • Forms a heterodimer with SLX4.

    Alternative splice isoforms for SLX1A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLX1A Gene

Post-translational modifications for SLX1A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SLX1A Gene

No data available for DME Specific Peptides for SLX1A Gene

Domains & Families for SLX1A Gene

Gene Families for SLX1A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SLX1A Gene

Graphical View of Domain Structure for InterPro Entry

Q9BQ83

UniProtKB/Swiss-Prot:

SLX1_HUMAN :
  • Belongs to the SLX1 family.
Family:
  • Belongs to the SLX1 family.
genes like me logo Genes that share domains with SLX1A: view

No data available for Suggested Antigen Peptide Sequences for SLX1A Gene

Function for SLX1A Gene

Molecular function for SLX1A Gene

UniProtKB/Swiss-Prot Function:
Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products.

Enzyme Numbers (IUBMB) for SLX1A Gene

Phenotypes From GWAS Catalog for SLX1A Gene

Gene Ontology (GO) - Molecular Function for SLX1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004518 nuclease activity IEA --
GO:0004519 endonuclease activity IEA --
GO:0005515 protein binding IPI 19595721
GO:0008821 crossover junction endodeoxyribonuclease activity IBA,IDA 19595721
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with SLX1A: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLX1A

No data available for Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SLX1A Gene

Localization for SLX1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLX1A Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLX1A gene
Compartment Confidence
nucleus 5
cytoskeleton 1
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SLX1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0033557 Slx1-Slx4 complex TAS 24012755
genes like me logo Genes that share ontologies with SLX1A: view

Pathways & Interactions for SLX1A Gene

genes like me logo Genes that share pathways with SLX1A: view

Gene Ontology (GO) - Biological Process for SLX1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000724 double-strand break repair via homologous recombination IBA,IMP 19595721
GO:0006281 DNA repair IMP 19595721
GO:0006310 DNA recombination IEA --
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0010792 DNA double-strand break processing involved in repair via single-strand annealing IMP 19595721
genes like me logo Genes that share ontologies with SLX1A: view

No data available for SIGNOR curated interactions for SLX1A Gene

Drugs & Compounds for SLX1A Gene

No Compound Related Data Available

Transcripts for SLX1A Gene

mRNA/cDNA for SLX1A Gene

2 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLX1A

Alternative Splicing Database (ASD) splice patterns (SP) for SLX1A Gene

No ASD Table

Relevant External Links for SLX1A Gene

GeneLoc Exon Structure for
SLX1A

Expression for SLX1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SLX1A Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLX1A Gene



Protein tissue co-expression partners for SLX1A Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SLX1A

SOURCE GeneReport for Unigene cluster for SLX1A Gene:

Hs.729791

Evidence on tissue expression from TISSUES for SLX1A Gene

  • Lung(4.1)
genes like me logo Genes that share expression patterns with SLX1A: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SLX1A Gene

Orthologs for SLX1A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SLX1A Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia -- 30
  • 99 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia SLX1A 29
  • 85.66 (n)
-- 30
  • 79 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia SLX1A 29 30
  • 83.65 (n)
OneToMany
Mouse
(Mus musculus)
Mammalia Slx1b 29 30
  • 77.53 (n)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Slx1b 29
  • 77.53 (n)
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 64 (a)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 62 (a)
OneToMany
Chicken
(Gallus gallus)
Aves -- 30
  • 31 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 51 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia slx1a 29
  • 61.03 (n)
Zebrafish
(Danio rerio)
Actinopterygii LOC100001845 29
  • 56.13 (n)
SLX1A 30
  • 47 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002259 29
  • 55.73 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta slx1 29 30
  • 52.46 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea slx-1 29 30
  • 46.9 (n)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SLX1 30
  • 21 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 42 (a)
OneToMany
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes slx1 29
  • 39.87 (n)
Species where no ortholog for SLX1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • 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)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SLX1A Gene

ENSEMBL:
Gene Tree for SLX1A (if available)
TreeFam:
Gene Tree for SLX1A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SLX1A: view image
Alliance of Genome Resources:
Additional Orthologs for SLX1A

Paralogs for SLX1A Gene

Paralogs for SLX1A Gene

(2) SIMAP similar genes for SLX1A Gene using alignment to 2 proteins:

  • SLX1_HUMAN
  • H3BPC3_HUMAN

Pseudogenes.org Pseudogenes for SLX1A Gene

genes like me logo Genes that share paralogs with SLX1A: view

Variants for SLX1A Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SLX1A Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SLX1A Gene

Variant ID Type Subtype PubMed ID
dgv1515e59 CNV duplication 20981092
esv22245 CNV gain 19812545
esv2714183 CNV deletion 23290073
esv2758641 CNV gain 17122850
esv2758642 CNV gain 17122850
esv29892 CNV gain 19812545
esv3333204 CNV duplication 20981092
esv3388213 CNV duplication 20981092
esv3392583 CNV duplication 20981092
esv3406739 CNV duplication 20981092
nsv1056249 CNV gain 25217958
nsv1078392 CNV duplication 25765185
nsv1078393 CNV duplication 25765185
nsv1139652 CNV duplication 24896259
nsv1141284 CNV duplication 24896259
nsv1146152 CNV duplication 26484159
nsv1150245 CNV duplication 26484159
nsv471387 CNV gain 19718026
nsv471388 CNV gain 19718026
nsv471389 CNV gain 19718026
nsv498862 CNV loss 21111241
nsv571809 CNV loss 21841781
nsv571810 CNV loss 21841781
nsv571819 CNV gain 21841781
nsv820959 CNV duplication 20802225
nsv821543 CNV duplication 20802225
nsv9426 CNV gain 18304495
nsv9431 CNV gain+loss 18304495
nsv960011 CNV duplication 23825009
nsv977954 CNV duplication 23825009
nsv978130 CNV duplication 23825009

Variation tolerance for SLX1A Gene

Gene Damage Index Score: 2.07; 37.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLX1A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLX1A
Leiden Open Variation Database (LOVD)
SLX1A

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLX1A Gene

Disorders for SLX1A Gene

MalaCards: The human disease database

(8) MalaCards diseases for SLX1A Gene - From: COP

Additional Disease Information for SLX1A

genes like me logo Genes that share disorders with SLX1A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLX1A Gene

Publications for SLX1A Gene

  1. Coordination of structure-specific nucleases by human SLX4/BTBD12 is required for DNA repair. (PMID: 19595721) Muñoz IM … Rouse J (Molecular cell 2009) 2 3 4
  2. Human SULT1A3 pharmacogenetics: gene duplication and functional genomic studies. (PMID: 15358107) Hildebrandt MA … Weinshilboum RM (Biochemical and biophysical research communications 2004) 2 3 4
  3. Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. (PMID: 19596236) Fekairi S … Gaillard PHL (Cell 2009) 3 4
  4. Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair. (PMID: 19596235) Svendsen JM … Harper JW (Cell 2009) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for SLX1A Gene

Sources for SLX1A Gene