Slx4 SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae) [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Slx4provided by MGI
Official Full Name: SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)provided by MGI
Primary source: MGI:MGI:106299
See related: Ensembl:ENSMUSG00000039738 AllianceGenome:MGI:106299
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Btbd12; D16Bwg1016e
Summary: This gene encodes a protein containing a BTB (POZ) domain that comprises a subunit of structure-specific endonucleases. The encoded protein aids in the resolution of DNA secondary structures that arise during the processes of DNA repair and recombination. Knock out of this gene in mouse recapitulates the phenotype of the human disease Fanconi anemia, including blood cytopenia and susceptibility to genomic instability. [provided by RefSeq, Dec 2013]
Expression: Ubiquitous expression in testis adult (RPKM 20.8), thymus adult (RPKM 7.0) and 25 other tissues See more
Orthologs: human all
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Genomic context

Location:: 16 A1; 16 2.34 cM

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	16	NC_000082.7 (3796969..3821708, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	16	NC_000082.6 (3979105..4003829, complement)

Chromosome 16 - NC_000082.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The structure-specific endonuclease complex SLX4-XPF regulates Tus-Ter-induced homologous recombination.
Title: The structure-specific endonuclease complex SLX4-XPF regulates Tus-Ter-induced homologous recombination.
Data shed light on SLX4 recruitment, and they point to the existence of currently unidentified ubiquitylated ligands and E3 ligases that are crucial for ICL repair.
Title: Distinct functional roles for the two SLX4 ubiquitin-binding UBZ domains mutated in Fanconi anemia.
SLX4 is a tumor suppressor, which activates XPF-ERCC1 nuclease specificity in DNA crosslink repair.
Title: Mouse SLX4 is a tumor suppressor that stimulates the activity of the nuclease XPF-ERCC1 in DNA crosslink repair.
Data indicate that SLX1 and MUS81-EME1 nucleases act together to resolve Holliday junctions (HJs) in a manner that requires tethering to SLX4.
Title: Cooperative control of holliday junction resolution and DNA repair by the SLX1 and MUS81-EME1 nucleases.
these data indicate that BTBD12 functions throughout gametogenesis to maintain genome stability, possibly by co-ordinating repair processes and/or by linking DNA repair events to the cell cycle via ATM
Title: Mammalian BTBD12 (SLX4) protects against genomic instability during mammalian spermatogenesis.
mouse Slx4, a regulator of structure-specific nucleases, disruption phenocopies Fanconi anemia
Title: Disruption of mouse Slx4, a regulator of structure-specific nucleases, phenocopies Fanconi anemia.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (4) 1 citation
Chemically induced (ENU) (1)
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI426760 (e-PCR)
- UniSTS:160518

R75086 (e-PCR)
- UniSTS:125533

RH136056 (e-PCR)
- UniSTS:210051

RH125161 (e-PCR)
- UniSTS:161983

D16Bwg1016e (e-PCR), detects polymorphism
- UniSTS:142037

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables enzyme activator activity	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IEA Inferred from Electronic Annotation more info
involved_in DNA double-strand break processing involved in repair via single-strand annealing	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within DNA recombination	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of telomere maintenance via telomere lengthening	ISO Inferred from Sequence Orthology more info
involved_in nucleotide-excision repair	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of t-circle formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of telomere maintenance	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in t-circle formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in t-circle formation	ISO Inferred from Sequence Orthology more info
involved_in telomeric D-loop disassembly	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of ERCC4-ERCC1 complex	ISO Inferred from Sequence Orthology more info
part_of Holliday junction resolvase complex	ISO Inferred from Sequence Orthology more info
part_of Slx1-Slx4 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Slx1-Slx4 complex	ISO Inferred from Sequence Orthology more info
located_in cell junction	ISO Inferred from Sequence Orthology more info
part_of chromatin	ISO Inferred from Sequence Orthology more info
colocalizes_with chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
located_in chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation 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.

mRNA and Protein(s)

NM_001402923.1 → NP_001389852.1 structure-specific endonuclease subunit SLX4 isoform 2

Status: REVIEWED

Source sequence(s)

AC087900
NM_001402924.1 → NP_001389853.1 structure-specific endonuclease subunit SLX4 isoform 2

Status: REVIEWED

Source sequence(s)

AC087900
NM_001402925.1 → NP_001389854.1 structure-specific endonuclease subunit SLX4 isoform 2

Status: REVIEWED

Source sequence(s)

AC087900
NM_001402926.1 → NP_001389855.1 structure-specific endonuclease subunit SLX4 isoform 3

Status: REVIEWED

Source sequence(s)

AC087900
NM_001402927.1 → NP_001389856.1 structure-specific endonuclease subunit SLX4 isoform 4

Status: REVIEWED

Source sequence(s)

AC087900
NM_001402928.1 → NP_001389857.1 structure-specific endonuclease subunit SLX4 isoform 4

Status: REVIEWED

Source sequence(s)

AC087900
NM_001402930.1 → NP_001389859.1 structure-specific endonuclease subunit SLX4 isoform 4

Status: REVIEWED

Source sequence(s)

AC087900
NM_001402931.1 → NP_001389860.1 structure-specific endonuclease subunit SLX4 isoform 4

Status: REVIEWED

Source sequence(s)

AC087900
NM_177472.5 → NP_803423.2 structure-specific endonuclease subunit SLX4 isoform 1

See identical proteins and their annotated locations for NP_803423.2

Status: REVIEWED

Source sequence(s)

BC065125, BC082337

Consensus CDS

CCDS37240.1

UniProtKB/Swiss-Prot

Q6P1D7

UniProtKB/TrEMBL

Q69ZA3

Related

ENSMUSP00000038871.8, ENSMUST00000040790.14

Conserved Domains (4) summary

smart00225
Location:507 → 603

BTB; Broad-Complex, Tramtrack and Bric a brac

pfam00651
Location:496 → 603

BTB; BTB/POZ domain

pfam09494
Location:1485 → 1541

Slx4; Slx4 endonuclease

cl21528
Location:570 → 680

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

RNA

NR_175318.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC087900

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000082.7 Reference GRCm39 C57BL/6J

Range

3796969..3821708 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006522354.4 → XP_006522417.1 structure-specific endonuclease subunit SLX4 isoform X3

See identical proteins and their annotated locations for XP_006522417.1

UniProtKB/TrEMBL

Q69ZA3

Conserved Domains (3) summary

cl38908
Location:526 → 640

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1565 → 1622

Slx4; Slx4 endonuclease

cl21528
Location:608 → 718

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
XM_006522352.2 → XP_006522415.1 structure-specific endonuclease subunit SLX4 isoform X3

See identical proteins and their annotated locations for XP_006522415.1

UniProtKB/TrEMBL

Q69ZA3

Conserved Domains (3) summary

cl38908
Location:526 → 640

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1565 → 1622

Slx4; Slx4 endonuclease

cl21528
Location:608 → 718

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
XM_030249182.2 → XP_030105042.1 structure-specific endonuclease subunit SLX4 isoform X7

UniProtKB/TrEMBL

Q69ZA3

Conserved Domains (3) summary

cl38908
Location:305 → 419

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1344 → 1401

Slx4; Slx4 endonuclease

cl21528
Location:387 → 497

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
XM_030249178.2 → XP_030105038.1 structure-specific endonuclease subunit SLX4 isoform X1

Conserved Domains (3) summary

cl38908
Location:603 → 717

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1642 → 1699

Slx4; Slx4 endonuclease

cl21528
Location:685 → 795

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
XM_030249185.2 → XP_030105045.1 structure-specific endonuclease subunit SLX4 isoform X7

UniProtKB/TrEMBL

Q69ZA3

Conserved Domains (3) summary

cl38908
Location:305 → 419

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1344 → 1401

Slx4; Slx4 endonuclease

cl21528
Location:387 → 497

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
XM_006522349.4 → XP_006522412.1 structure-specific endonuclease subunit SLX4 isoform X1

See identical proteins and their annotated locations for XP_006522412.1

Conserved Domains (3) summary

cl38908
Location:603 → 717

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1642 → 1699

Slx4; Slx4 endonuclease

cl21528
Location:685 → 795

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
XM_030249177.1 → XP_030105037.1 structure-specific endonuclease subunit SLX4 isoform X1

Conserved Domains (3) summary

cl38908
Location:603 → 717

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1642 → 1699

Slx4; Slx4 endonuclease

cl21528
Location:685 → 795

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
XM_006522355.3 → XP_006522418.1 structure-specific endonuclease subunit SLX4 isoform X4

UniProtKB/TrEMBL

Q69ZA3

Conserved Domains (3) summary

cl38908
Location:450 → 564

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1489 → 1546

Slx4; Slx4 endonuclease

cl21528
Location:532 → 642

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
XM_030249183.1 → XP_030105043.1 structure-specific endonuclease subunit SLX4 isoform X7

UniProtKB/TrEMBL

Q69ZA3

Conserved Domains (3) summary

cl38908
Location:305 → 419

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1344 → 1401

Slx4; Slx4 endonuclease

cl21528
Location:387 → 497

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
XM_030249187.2 → XP_030105047.1 structure-specific endonuclease subunit SLX4 isoform X9

Conserved Domains (1) summary

pfam09494
Location:943 → 1000

Slx4; Slx4 endonuclease
XM_006522350.3 → XP_006522413.1 structure-specific endonuclease subunit SLX4 isoform X1

See identical proteins and their annotated locations for XP_006522413.1

Conserved Domains (3) summary

cl38908
Location:603 → 717

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1642 → 1699

Slx4; Slx4 endonuclease

cl21528
Location:685 → 795

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
XM_030249186.1 → XP_030105046.1 structure-specific endonuclease subunit SLX4 isoform X7

UniProtKB/TrEMBL

Q69ZA3

Conserved Domains (3) summary

cl38908
Location:305 → 419

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1344 → 1401

Slx4; Slx4 endonuclease

cl21528
Location:387 → 497

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
XM_006522353.1 → XP_006522416.1 structure-specific endonuclease subunit SLX4 isoform X3

See identical proteins and their annotated locations for XP_006522416.1

UniProtKB/TrEMBL

Q69ZA3

Conserved Domains (3) summary

cl38908
Location:526 → 640

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

pfam09494
Location:1565 → 1622

Slx4; Slx4 endonuclease

cl21528
Location:608 → 718

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
XM_017317068.2 → XP_017172557.1 structure-specific endonuclease subunit SLX4 isoform X11

Conserved Domains (2) summary

PTZ00449
Location:518 → 767

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

pfam09494
Location:820 → 877

Slx4; Slx4 endonuclease
XM_006522359.2 → XP_006522422.1 structure-specific endonuclease subunit SLX4 isoform X10

Conserved Domains (2) summary

PTZ00449
Location:518 → 742

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

pfam09494
Location:863 → 920

Slx4; Slx4 endonuclease
XM_030249181.2 → XP_030105041.1 structure-specific endonuclease subunit SLX4 isoform X6

Conserved Domains (2) summary

cl38908
Location:603 → 717

BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily

cl21528
Location:685 → 795

Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family