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

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: mouse all
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Genomic context

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_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Polyubiquitinated PCNA triggers SLX4-mediated break-induced replication in alternative lengthening of telomeres (ALT) cancer cells.
Title: Polyubiquitinated PCNA triggers SLX4-mediated break-induced replication in alternative lengthening of telomeres (ALT) cancer cells.
Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair.
Title: Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair.
RNF168 E3 ligase participates in ubiquitin signaling and recruitment of SLX4 during DNA crosslink repair.
Title: RNF168 E3 ligase participates in ubiquitin signaling and recruitment of SLX4 during DNA crosslink repair.
Coordinated roles of SLX4 and MutSbeta in DNA repair and the maintenance of genome stability.
Title: Coordinated roles of SLX4 and MutSβ in DNA repair and the maintenance of genome stability.
Abraxas suppresses DNA end resection and limits break-induced replication by controlling SLX4/MUS81 chromatin loading in response to TOP1 inhibitor-induced DNA damage.
Title: Abraxas suppresses DNA end resection and limits break-induced replication by controlling SLX4/MUS81 chromatin loading in response to TOP1 inhibitor-induced DNA damage.
PARP1 modulates telomere sister chromatid exchange and telomere length homeostasis by regulating telomere localization of SLX4 in U2OS cells.
Title: PARP1 modulates telomere sister chromatid exchange and telomere length homeostasis by regulating telomere localization of SLX4 in U2OS cells.
SLX4-XPF mediates DNA damage responses to replication stress induced by DNA-protein interactions.
Title: SLX4-XPF mediates DNA damage responses to replication stress induced by DNA-protein interactions.
SLX4 interacts with RTEL1 to prevent transcription-mediated DNA replication perturbations.
Title: SLX4 interacts with RTEL1 to prevent transcription-mediated DNA replication perturbations.
The binding of SLX4IP to both SLX4 and XPF-ERCC1 not only is vital for maintaining the stability of SLX4IP protein, but also promotes the interaction between SLX4 and XPF-ERCC1, especially after DNA damage. Collectively, these results demonstrate a new regulatory role for SLX4IP in maintaining an efficient SLX4-XPF-ERCC1 complex in interstrand crosslinks (ICLs) repair.
Title: SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair.
This review aims at providing an up-to-date and comprehensive view on the key functions that SLX4 fulfills to maintain genome stability as well as to highlight and discuss areas of uncertainty and emerging concepts. [review]
Title: SLX4: multitasking to maintain genome stability.

Submit: New GeneRIF Correction See all GeneRIFs (47)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Fanconi anemia complementation group P MedGen: C3469542 OMIM: 613951 GeneReviews: Fanconi Anemia	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

D8S2279 (e-PCR)
- UniSTS:473907

L18426 (e-PCR)
- UniSTS:34648

RH92116 (e-PCR)
- UniSTS:91227

D1S1423 (e-PCR)
- UniSTS:149619

NoName (e-PCR)
- UniSTS:486519

AFMa217xh1 (e-PCR)
- UniSTS:51901

SHGC-143024 (e-PCR)
- UniSTS:171767

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

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 DNA replication	IEA Inferred from Electronic Annotation 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 nucleotide-excision repair	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 positive regulation of telomere maintenance	IDA Inferred from Direct Assay more info	PubMed
involved_in resolution of meiotic recombination intermediates	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within response to intra-S DNA damage checkpoint signaling	IMP Inferred from Mutant Phenotype more info	PubMed
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 telomeric D-loop disassembly	IMP Inferred from Mutant Phenotype 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

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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

NG_028123.1 RefSeqGene

Range

5001..35404

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_503

mRNA and Protein(s)

NM_032444.4 → NP_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:673 → 787

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:1754 → 1810

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

3581181..3611606 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (3) summary

smart00225
Location:699 → 788

BTB; Broad-Complex, Tramtrack and Bric a brac

pfam09494
Location:1753 → 1809

Slx4; Slx4 endonuclease

cl02518
Location:681 → 788

BTB; BTB/POZ domain
XM_024450471.2 → XP_024306239.1 structure-specific endonuclease subunit SLX4 isoform X1

UniProtKB/Swiss-Prot

Q69YT8, Q8IY92, Q8TF15, Q96JP1

Conserved Domains (2) summary

cd18288
Location:673 → 787

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:1754 → 1810

Slx4; Slx4 endonuclease
XM_047434801.1 → XP_047290757.1 structure-specific endonuclease subunit SLX4 isoform X3

RNA

XR_007064923.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

3608449..3638875 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054314193.1 → XP_054170168.1 structure-specific endonuclease subunit SLX4 isoform X2
XM_054314192.1 → XP_054170167.1 structure-specific endonuclease subunit SLX4 isoform X1

UniProtKB/Swiss-Prot

Q69YT8, Q8IY92, Q8TF15, Q96JP1
XM_054314194.1 → XP_054170169.1 structure-specific endonuclease subunit SLX4 isoform X3