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    SLX1B SLX1 homolog B, structure-specific endonuclease subunit [ Homo sapiens (human) ]

    Gene ID: 79008, updated on 17-Jun-2024

    Summary

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    Official Symbol
    SLX1Bprovided by HGNC
    Official Full Name
    SLX1 homolog B, structure-specific endonuclease subunitprovided by HGNC
    Primary source
    HGNC:HGNC:28748
    See related
    Ensembl:ENSG00000181625 MIM:615823; AllianceGenome:HGNC:28748
    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
    GIYD2
    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 telomeric copy. Alternative splicing results in multiple transcript variants. Read-through transcription also occurs between this gene and the downstream SULT1A4 (sulfotransferase family, cytosolic, 1A, phenol-preferring, member 4) gene. [provided by RefSeq, Nov 2010]
    Expression
    Ubiquitous expression in duodenum (RPKM 33.7), small intestine (RPKM 28.9) and 24 other tissues See more
    Orthologs
    all
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    Genomic context

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    See SLX1B in Genome Data Viewer
    Location:
    16p11.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (29454533..29458220)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29736324..29740011)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (29465854..29469541)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene SMG1 pseudogene 6 Neighboring gene small nucleolar RNA U13 Neighboring gene BOLA2-SMG1P6 readthrough Neighboring gene coronin 1A pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:29465349-29466088 Neighboring gene SLX1B-SULT1A4 readthrough (NMD candidate) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29466829-29467566 Neighboring gene bolA family member 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29470053-29470888 Neighboring gene sulfotransferase family 1A member 4 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
    • 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. Human SULT1A3 pharmacogenetics: gene duplication and functional genomic studies. Hildebrandt MA, et al. Biochem Biophys Res Commun, 2004 Sep 3. PMID 15358107
    2. SLX4 assembles a telomere maintenance toolkit by bridging multiple endonucleases with telomeres. Wan B, et al. Cell Rep, 2013 Sep 12. PMID 24012755, Free PMC Article
    3. Drosophila MUS312 and the vertebrate ortholog BTBD12 interact with DNA structure-specific endonucleases in DNA repair and recombination. Andersen SL, et al. Mol Cell, 2009 Jul 10. PMID 19595722, Free PMC Article
    4. Coordination of structure-specific nucleases by human SLX4/BTBD12 is required for DNA repair. Muñoz IM, et al. Mol Cell, 2009 Jul 10. PMID 19595721
    5. Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Fekairi S, et al. Cell, 2009 Jul 10. PMID 19596236, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough SLX1B-SULT1A4

    Readthrough gene: SLX1B-SULT1A4, Included gene: SULT1A4

    Homology

    Clone Names

    • MGC2532, MGC5178, FLJ23439

    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 B

    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_001400286.1 → NP_001387215.1  structure-specific endonuclease subunit SLX1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC133555
      UniProtKB/TrEMBL
      Q9H5H2

    2. NM_001400287.1 → NP_001387216.1  structure-specific endonuclease subunit SLX1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC133555

    3. NM_024044.5 → NP_076949.1  structure-specific endonuclease subunit SLX1 isoform 1

      See identical proteins and their annotated locations for NP_076949.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC133555
      Consensus CDS
      CCDS10648.1
      UniProtKB/Swiss-Prot
      B7ZME1, Q6NTG6, Q9BQ83
      UniProtKB/TrEMBL
      Q9H5H2
      Related
      ENSP00000328940.5, ENST00000330181.10
      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

    4. NM_178044.4 → NP_835145.1  structure-specific endonuclease subunit SLX1 isoform 2

      See identical proteins and their annotated locations for NP_835145.1

      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)
      AC133555
      Consensus CDS
      CCDS10649.1
      UniProtKB/Swiss-Prot
      Q9BQ83
      Related
      ENSP00000335316.4, ENST00000351581.4
      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_2023_10

    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
      29454533..29458220
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      29736324..29740011
      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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