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Aliases for SLX1A Gene

Aliases for SLX1A Gene

  • SLX1 Homolog A, Structure-Specific Endonuclease Subunit 2 3 5
  • 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
  • Structure-Specific Endonuclease Subunit SLX1 3
  • GIY-YIG Domain Containing 1 2
  • SLX1A SLX1B 4
  • EC 3.1.-.- 4
  • 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
  • GC16P030222
  • GC16P030233
  • GC16P030242
  • GC16P030247
  • GC16P030252

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 Fanconi Anemia, Complementation Group A. Among its related pathways are DNA Double-Strand Break Repair and Fanconi anemia pathway. 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 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.

Additional gene information for SLX1A Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLX1A Gene

Genomics for SLX1A Gene

GeneHancer (GH) Regulatory Elements for SLX1A Gene

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
GH16I030193 Promoter/Enhancer 1.2 EPDnew Ensembl dbSUPER 550.8 +0.1 58 1.8 BOLA2B SLX1A SLX1A-SULT1A3 GC16P030195
GH16I030566 Promoter/Enhancer 2.3 FANTOM5 Ensembl ENCODE dbSUPER 63.6 +376.0 376031 6 ZFP64 FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 SP3 SETD1A SRCAP ENSG00000260267 FUS INO80E ZNF747 NPIPB13 ZNF764 SMG1P5 SMG1P2
GH16I030052 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 63.3 -139.6 -139638 3.1 CLOCK MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 FAM57B ALDOA SETD1A SRCAP NPIPB12 INO80E SMG1P5 SMG1P2 ZNF764 ZNF747
GH16I030192 Enhancer 0.2 dbSUPER 550.8 -1.5 -1519 0.3 SLX1A-SULT1A3 SLX1A BOLA2B ENSG00000261416
GH16I030200 Enhancer 0.2 dbSUPER 550.8 +1.4 1429 0.3 BOLA2B SLX1A-SULT1A3 SLX1A GC16P030195 SULT1A3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SLX1A on UCSC Golden Path with GeneCards custom track

Genomic Locations for SLX1A Gene

Genomic Locations for SLX1A Gene
chr16:30,193,843-30,197,566
(GRCh38/hg38)
Size:
3,724 bases
Orientation:
Plus strand
chr16:30,205,164-30,208,887
(GRCh37/hg19)

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.
    • 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

No Post-translational modifications

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:0004520 endodeoxyribonuclease activity TAS --
GO:0005515 protein binding IPI 19595721
GO:0008821 crossover junction endodeoxyribonuclease activity IDA 19595721
genes like me logo Genes that share ontologies with SLX1A: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , 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

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 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 :
(1) Additional mRNA sequences :
(6) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SLX1A Gene

SLX1 structure-specific endonuclease subunit homolog A (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

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

No ASD Table

Relevant External Links for SLX1A Gene

GeneLoc Exon Structure for
SLX1A
ECgene alternative splicing isoforms for
SLX1A

Expression for SLX1A Gene

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

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



Protein tissue co-expression partners for SLX1A Gene

NURSA nuclear receptor signaling pathways regulating expression of SLX1A Gene:

SLX1A

SOURCE GeneReport for Unigene cluster for SLX1A Gene:

Hs.729791

Evidence on tissue expression from TISSUES for SLX1A Gene

  • Lung(4)
genes like me logo Genes that share expression patterns with SLX1A: view

Primer Products

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 -- 34
  • 99 (a)
OneToMany
dog
(Canis familiaris)
Mammalia SLX1A 33
  • 85.66 (n)
-- 34
  • 79 (a)
OneToMany
cow
(Bos Taurus)
Mammalia SLX1A 33 34
  • 83.65 (n)
mouse
(Mus musculus)
Mammalia Slx1b 33 34
  • 77.53 (n)
rat
(Rattus norvegicus)
Mammalia Slx1b 33
  • 77.53 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 64 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 62 (a)
OneToMany
chicken
(Gallus gallus)
Aves -- 34
  • 31 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 51 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia slx1a 33
  • 61.03 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100001845 33
  • 56.13 (n)
SLX1A 34
  • 47 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002259 33
  • 55.73 (n)
fruit fly
(Drosophila melanogaster)
Insecta slx1 33 34
  • 52.46 (n)
worm
(Caenorhabditis elegans)
Secernentea slx-1 33 34
  • 46.9 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SLX1 34
  • 21 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 42 (a)
OneToMany
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes slx1 33
  • 39.87 (n)
Species where no ortholog for SLX1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for SLX1A Gene

Paralogs for SLX1A Gene

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

Pseudogenes.org Pseudogenes for SLX1A Gene

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

Variants for SLX1A Gene

Sequence variations from dbSNP and Humsavar for SLX1A Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1003660683 -- 30,194,786(+) C/T coding_sequence_variant, missense_variant
rs1005284345 -- 30,197,850(+) C/G downstream_transcript_variant
rs1012475256 -- 30,197,522(+) A/G 3_prime_UTR_variant
rs1012919487 -- 30,194,823(+) G/A/T intron_variant
rs1014971225 -- 30,197,882(+) G/A downstream_transcript_variant

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLX1A Gene

Disorders for SLX1A Gene

MalaCards: The human disease database

(1) MalaCards diseases for SLX1A Gene - From: DISEASES

Disorder Aliases PubMed IDs
fanconi anemia, complementation group a
  • fanca
- elite association - COSMIC cancer census association via MalaCards
Search SLX1A in MalaCards View complete list of genes associated with diseases

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 58
  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 58
  3. Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair. (PMID: 19596235) Svendsen JM … Harper JW (Cell 2009) 3 4 58
  4. Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. (PMID: 19596236) Fekairi S … Gaillard PH (Cell 2009) 3 4 58
  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 58

Products for SLX1A Gene

Sources for SLX1A Gene

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