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    SLX1A SLX1 homolog A, structure-specific endonuclease subunit [ Homo sapiens (human) ]

    Gene ID: 548593, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SLX1Aprovided by HGNC
    Official Full Name
    SLX1 homolog A, structure-specific endonuclease subunitprovided by HGNC
    Primary source
    HGNC:HGNC:20922
    See related
    Ensembl:ENSG00000132207 MIM:615822; AllianceGenome:HGNC:20922
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GIYD1
    Summary
    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]
    Expression
    Ubiquitous expression in duodenum (RPKM 34.0), small intestine (RPKM 29.1) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLX1A in Genome Data Viewer
    Location:
    16p11.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30193843..30197566)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (30478393..30482118)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30205164..30208887)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30195204-30195744 Neighboring gene CORO1A antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30195745-30196286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30196287-30196826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30196827-30197368 Neighboring gene coronin 1A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10695 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30197909-30198449 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30198450-30198989 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:30204716-30205440 Neighboring gene SLX1A-SULT1A3 readthrough (NMD candidate) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30206166-30206889 Neighboring gene bolA family member 2B Neighboring gene sulfotransferase family 1A member 3 Neighboring gene SAGA complex associated factor 29 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Folate stress induces SLX1- and RAD51-dependent mitotic DNA synthesis at the fragile X locus in human cells. Garribba L, et al. Proc Natl Acad Sci U S A, 2020 Jul 14. PMID 32601218, Free PMC Article
    2. Coordinated actions of SLX1-SLX4 and MUS81-EME1 for Holliday junction resolution in human cells. Wyatt HD, et al. Mol Cell, 2013 Oct 24. PMID 24076221
    3. Regulation of multiple DNA repair pathways by the Fanconi anemia protein SLX4. Kim Y, et al. Blood, 2013 Jan 3. PMID 23093618, Free PMC Article
    4. Human SULT1A3 pharmacogenetics: gene duplication and functional genomic studies. Hildebrandt MA, et al. Biochem Biophys Res Commun, 2004 Sep 3. PMID 15358107
    5. SLX4-SLX1 Protein-independent Down-regulation of MUS81-EME1 Protein by HIV-1 Viral Protein R (Vpr). Zhou X, et al. J Biol Chem, 2016 Aug 12. PMID 27354282, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Folate stress induces SLX1- and RAD51-dependent mitotic DNA synthesis at the fragile X locus in human cells.
      Title: Folate stress induces SLX1- and RAD51-dependent mitotic DNA synthesis at the fragile X locus in human cells.
    2. SLX4-SLX1 Protein-independent Down-regulation of MUS81-EME1 Protein by HIV-1 Viral Protein R (Vpr).
      Title: SLX4-SLX1 Protein-independent Down-regulation of MUS81-EME1 Protein by HIV-1 Viral Protein R (Vpr).
    3. Data show that three structure-selective endonucleases, SLX1-SLX4, MUS81-EME1, and GEN1, define two pathways of Holliday junctions (HJs) resolution in HeLa cells.
      Title: Coordinated actions of SLX1-SLX4 and MUS81-EME1 for Holliday junction resolution in human cells.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough SLX1A-SULT1A3

    Readthrough gene: SLX1A-SULT1A3, Included gene: SULT1A3

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5'-flap endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 5'-flap endonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables crossover junction DNA endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables crossover junction DNA endonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA double-strand break processing involved in repair via single-strand annealing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in double-strand break repair via homologous recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in double-strand break repair via homologous recombination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of telomere maintenance via telomere lengthening IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of t-circle formation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in t-circle formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in t-circle formation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in telomere maintenance via telomere lengthening IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in telomeric D-loop disassembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Slx1-Slx4 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Slx1-Slx4 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Slx1-Slx4 complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    structure-specific endonuclease subunit SLX1
    Names
    GIY-YIG domain-containing protein 1
    SLX1 structure-specific endonuclease subunit homolog A

    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)

    1. NM_001014999.3 → NP_001014999.1  structure-specific endonuclease subunit SLX1 isoform 1

      See identical proteins and their annotated locations for NP_001014999.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AI885276, BC144462, BI757439, CD673028
      Consensus CDS
      CCDS32431.1
      UniProtKB/Swiss-Prot
      B7ZME1, Q6NTG6, Q9BQ83
      UniProtKB/TrEMBL
      Q9H5H2
      Related
      ENSP00000251303.7, ENST00000251303.11
      Conserved Domains (1) summary
      cd10455
      Location:13 → 89
      GIY-YIG_SLX1; Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its eukaryotic homologs

    2. NM_001015000.2 → NP_001015000.1  structure-specific endonuclease subunit SLX1 isoform 2

      See identical proteins and their annotated locations for NP_001015000.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AI885276, BC144462, BI757439
      Consensus CDS
      CCDS32432.1
      UniProtKB/Swiss-Prot
      Q9BQ83
      Related
      ENSP00000333945.4, ENST00000345535.9
      Conserved Domains (1) summary
      cd10455
      Location:13 → 82
      GIY-YIG_SLX1; Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its eukaryotic homologs

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      30193843..30197566
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      30478393..30482118
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BQ83.1 GenPept UniProtKB/Swiss-Prot:Q9BQ83

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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