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

    Gene ID: 548593, updated on 10-Dec-2024

    Summary

    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
    NEW
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    Try the new Transcript table

    Genomic context

    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

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Readthrough SLX1A-SULT1A3

    Readthrough gene: SLX1A-SULT1A3, Included gene: SULT1A3

    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 
    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

    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)

    NEW Try the new Transcript table

    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_001014999.3NP_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:1389
      GIY-YIG_SLX1; Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its eukaryotic homologs
    2. NM_001015000.2NP_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:1382
      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)