U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 79008, updated on 7-Apr-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
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)

Go to the top of the page Help

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

    Status: REVIEWED

    Source sequence(s)
    AC133555

  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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous