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

Gene ID: 548593, updated on 2-Mar-2021

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
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
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Genomic context

See SLX1A in Genome Data Viewer
Location:
16p11.2
Exon count:
6
Annotation release Status Assembly Chr Location
109.20210226 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (30193843..30197566)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30205164..30208887)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene CORO1A antisense RNA 1 Neighboring gene coronin 1A Neighboring gene SLX1A-SULT1A3 readthrough (NMD candidate) 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

Homology

Gene Ontology Provided by GOA

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

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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_001014999.3NP_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
    Q9BQ83
    Related
    ENSP00000251303.6, ENST00000251303.10
    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, ENST00000345535.8
    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: Homo sapiens Updated Annotation Release 109.20210226

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

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