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

Gene ID: 52864, updated on 21-Apr-2024

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
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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_000082.7Genomic Context describing neighboring genes Neighboring gene clusterin associated protein 1 Neighboring gene predicted gene, 57636 Neighboring gene NLR family, CARD domain containing 3 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:3976439-3976665 Neighboring gene STARR-seq mESC enhancer starr_39914 Neighboring gene deoxyribonuclease I Neighboring gene TNF receptor-associated protein 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:4077725-4077912 Neighboring gene CREB binding protein Neighboring gene STARR-seq mESC enhancer starr_39921

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (4)  1 citation
  • Chemically induced (ENU) (1) 
  • Endonuclease-mediated (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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)

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

    Status: REVIEWED

    Source sequence(s)
    AC087900
  2. NM_001402924.1NP_001389853.1  structure-specific endonuclease subunit SLX4 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC087900
  3. NM_001402925.1NP_001389854.1  structure-specific endonuclease subunit SLX4 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC087900
  4. NM_001402926.1NP_001389855.1  structure-specific endonuclease subunit SLX4 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC087900
  5. NM_001402927.1NP_001389856.1  structure-specific endonuclease subunit SLX4 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC087900
  6. NM_001402928.1NP_001389857.1  structure-specific endonuclease subunit SLX4 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC087900
  7. NM_001402930.1NP_001389859.1  structure-specific endonuclease subunit SLX4 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC087900
  8. NM_001402931.1NP_001389860.1  structure-specific endonuclease subunit SLX4 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC087900
  9. NM_177472.5NP_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:507603
    BTB; Broad-Complex, Tramtrack and Bric a brac
    pfam00651
    Location:496603
    BTB; BTB/POZ domain
    pfam09494
    Location:14851541
    Slx4; Slx4 endonuclease
    cl21528
    Location:570680
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

RNA

  1. 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

  1. NC_000082.7 Reference GRCm39 C57BL/6J

    Range
    3796969..3821708 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006522354.4XP_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:526640
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    pfam09494
    Location:15651622
    Slx4; Slx4 endonuclease
    cl21528
    Location:608718
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  2. XM_006522352.2XP_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:526640
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    pfam09494
    Location:15651622
    Slx4; Slx4 endonuclease
    cl21528
    Location:608718
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  3. XM_030249182.2XP_030105042.1  structure-specific endonuclease subunit SLX4 isoform X7

    UniProtKB/TrEMBL
    Q69ZA3
    Conserved Domains (3) summary
    cl38908
    Location:305419
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    pfam09494
    Location:13441401
    Slx4; Slx4 endonuclease
    cl21528
    Location:387497
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  4. XM_030249178.2XP_030105038.1  structure-specific endonuclease subunit SLX4 isoform X1

    Conserved Domains (3) summary
    cl38908
    Location:603717
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    pfam09494
    Location:16421699
    Slx4; Slx4 endonuclease
    cl21528
    Location:685795
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  5. XM_030249185.2XP_030105045.1  structure-specific endonuclease subunit SLX4 isoform X7

    UniProtKB/TrEMBL
    Q69ZA3
    Conserved Domains (3) summary
    cl38908
    Location:305419
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    pfam09494
    Location:13441401
    Slx4; Slx4 endonuclease
    cl21528
    Location:387497
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  6. XM_006522349.4XP_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:603717
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    pfam09494
    Location:16421699
    Slx4; Slx4 endonuclease
    cl21528
    Location:685795
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  7. XM_030249177.1XP_030105037.1  structure-specific endonuclease subunit SLX4 isoform X1

    Conserved Domains (3) summary
    cl38908
    Location:603717
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    pfam09494
    Location:16421699
    Slx4; Slx4 endonuclease
    cl21528
    Location:685795
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  8. XM_006522355.3XP_006522418.1  structure-specific endonuclease subunit SLX4 isoform X4

    UniProtKB/TrEMBL
    Q69ZA3
    Conserved Domains (3) summary
    cl38908
    Location:450564
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    pfam09494
    Location:14891546
    Slx4; Slx4 endonuclease
    cl21528
    Location:532642
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  9. XM_030249183.1XP_030105043.1  structure-specific endonuclease subunit SLX4 isoform X7

    UniProtKB/TrEMBL
    Q69ZA3
    Conserved Domains (3) summary
    cl38908
    Location:305419
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    pfam09494
    Location:13441401
    Slx4; Slx4 endonuclease
    cl21528
    Location:387497
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  10. XM_030249187.2XP_030105047.1  structure-specific endonuclease subunit SLX4 isoform X9

    Conserved Domains (1) summary
    pfam09494
    Location:9431000
    Slx4; Slx4 endonuclease
  11. XM_006522350.3XP_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:603717
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    pfam09494
    Location:16421699
    Slx4; Slx4 endonuclease
    cl21528
    Location:685795
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  12. XM_030249186.1XP_030105046.1  structure-specific endonuclease subunit SLX4 isoform X7

    UniProtKB/TrEMBL
    Q69ZA3
    Conserved Domains (3) summary
    cl38908
    Location:305419
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    pfam09494
    Location:13441401
    Slx4; Slx4 endonuclease
    cl21528
    Location:387497
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  13. XM_006522353.1XP_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:526640
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    pfam09494
    Location:15651622
    Slx4; Slx4 endonuclease
    cl21528
    Location:608718
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  14. XM_017317068.2XP_017172557.1  structure-specific endonuclease subunit SLX4 isoform X11

    Conserved Domains (2) summary
    PTZ00449
    Location:518767
    PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
    pfam09494
    Location:820877
    Slx4; Slx4 endonuclease
  15. XM_006522359.2XP_006522422.1  structure-specific endonuclease subunit SLX4 isoform X10

    Conserved Domains (2) summary
    PTZ00449
    Location:518742
    PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
    pfam09494
    Location:863920
    Slx4; Slx4 endonuclease
  16. XM_030249181.2XP_030105041.1  structure-specific endonuclease subunit SLX4 isoform X6

    Conserved Domains (2) summary
    cl38908
    Location:603717
    BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
    cl21528
    Location:685795
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

RNA

  1. XR_004939200.1 RNA Sequence

  2. XR_003951798.2 RNA Sequence