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SLX4 SLX4 structure-specific endonuclease subunit [ Homo sapiens (human) ]

Gene ID: 84464, updated on 9-Dec-2024

Summary

Official Symbol
SLX4provided by HGNC
Official Full Name
SLX4 structure-specific endonuclease subunitprovided by HGNC
Primary source
HGNC:HGNC:23845
See related
Ensembl:ENSG00000188827 MIM:613278; AllianceGenome:HGNC:23845
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
FANCP; BTBD12; MUS312
Summary
This gene encodes a protein that functions as an assembly component of multiple structure-specific endonucleases. These endonuclease complexes are required for repair of specific types of DNA lesions and critical for cellular responses to replication fork failure. Mutations in this gene were found in patients with Fanconi anemia. [provided by RefSeq, Sep 2016]
Expression
Broad expression in testis (RPKM 5.9), lymph node (RPKM 2.0) and 22 other tissues See more
Orthologs
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Genomic context

See SLX4 in Genome Data Viewer
Location:
16p13.3
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (3581181..3611606, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (3608449..3638875, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (3631182..3661607, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3594423-3594923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10326 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3602829-3603548 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3603549-3604269 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3604270-3604989 Neighboring gene NLR family CARD domain containing 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3611863-3612363 Neighboring gene uncharacterized LOC124903632 Neighboring gene uncharacterized LOC105371060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3630649-3631444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3639498-3640244 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10331 Neighboring gene deoxyribonuclease 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3690553-3691412 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3691413-3692270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3692271-3693129 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3694284-3695037 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3695038-3695790 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3695791-3696544 Neighboring gene uncharacterized LOC124903631 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3704869-3705396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3705397-3705924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3721637-3722136 Neighboring gene uncharacterized LOC124903630 Neighboring gene TNF receptor associated protein 1

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?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr-mediated cell cycle G2/M arrest requires human SLX4, MUS81, and EME1 proteins in cells PubMed
vpr The targeting of active SLX4 by HIV-1 Vpr to HIV-1 DNA serves as a viral strategy to avoid innate immune sensing PubMed
vpr VPRBP is required for HIV-1 Vpr-mediated activation of the SLX4 complex and modulation of MUS81 levels. The interaction between Vpr and VPRBP is involved in MUS81 ubiquitination PubMed
vpr HIV-1 Vpr induces untimely activation of SLX4-associated MUS81-EME1 through phosphorylation of EME1 by PLK1 PubMed
vpr HIV-1 Vpr directly interacts with the C-terminal SLX1 binding domain of SLX4 and recruits VPRBP to the SSE regulator complex SLX4 PubMed
vpr Co-immunoprecipitation and glycerol-gradient sedimentation demonstrate that HIV-1 Vpr, VPRBP, DDB1, SLX4, MUS81, EME1, ERCC1, and ERCC4 form a complex PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • KIAA1784, KIAA1987

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables enzyme activator 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 ERCC4-ERCC1 complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of Holliday junction resolvase complex IDA
Inferred from Direct Assay
more info
PubMed 
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 cell junction IDA
Inferred from Direct Assay
more info
 
located_in chromatin IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
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 SLX4
Names
BTB/POZ domain-containing protein 12

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.

Genomic

  1. NG_028123.1 RefSeqGene

    Range
    5001..35404
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_503

mRNA and Protein(s)

  1. NM_032444.4NP_115820.2  structure-specific endonuclease subunit SLX4

    See identical proteins and their annotated locations for NP_115820.2

    Status: REVIEWED

    Source sequence(s)
    AA279053, AC006111, AI380342, AK095411, AL442083, BC029952, BE887716, BM541728, DA242337, HY050233, HY246029
    Consensus CDS
    CCDS10506.2
    UniProtKB/Swiss-Prot
    Q69YT8, Q8IY92, Q8TF15, Q96JP1
    Related
    ENSP00000294008.3, ENST00000294008.4
    Conserved Domains (2) summary
    cd18288
    Location:673787
    BTB_POZ_BTBD12_SLX4; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Structure-specific endonuclease subunit SLX4
    pfam09494
    Location:17541810
    Slx4; Slx4 endonuclease

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
    3581181..3611606 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522715.4XP_011521017.1  structure-specific endonuclease subunit SLX4 isoform X2

    Conserved Domains (3) summary
    smart00225
    Location:699788
    BTB; Broad-Complex, Tramtrack and Bric a brac
    pfam09494
    Location:17531809
    Slx4; Slx4 endonuclease
    cl02518
    Location:681788
    BTB; BTB/POZ domain
  2. XM_024450471.2XP_024306239.1  structure-specific endonuclease subunit SLX4 isoform X1

    UniProtKB/Swiss-Prot
    Q69YT8, Q8IY92, Q8TF15, Q96JP1
    Conserved Domains (2) summary
    cd18288
    Location:673787
    BTB_POZ_BTBD12_SLX4; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Structure-specific endonuclease subunit SLX4
    pfam09494
    Location:17541810
    Slx4; Slx4 endonuclease
  3. XM_047434801.1XP_047290757.1  structure-specific endonuclease subunit SLX4 isoform X3

RNA

  1. XR_007064923.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    3608449..3638875 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314193.1XP_054170168.1  structure-specific endonuclease subunit SLX4 isoform X2

  2. XM_054314192.1XP_054170167.1  structure-specific endonuclease subunit SLX4 isoform X1

    UniProtKB/Swiss-Prot
    Q69YT8, Q8IY92, Q8TF15, Q96JP1
  3. XM_054314194.1XP_054170169.1  structure-specific endonuclease subunit SLX4 isoform X3