Mouse Gene Slx4 (ENSMUST00000040790.13) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae) (Slx4), mRNA. (from RefSeq NM_177472)
RefSeq Summary (NM_177472): 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].
Gencode Transcript: ENSMUST00000040790.13
Gencode Gene: ENSMUSG00000039738.16
Transcript (Including UTRs)
   Position: mm10 chr16:3,979,123-4,001,680 Size: 22,558 Total Exon Count: 15 Strand: -
Coding Region
   Position: mm10 chr16:3,979,821-4,001,370 Size: 21,550 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:3,979,123-4,001,680)mRNA (may differ from genome)Protein (1565 aa)
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-  Comments and Description Text from UniProtKB
  ID: SLX4_MOUSE
DESCRIPTION: RecName: Full=Structure-specific endonuclease subunit SLX4; AltName: Full=BTB/POZ domain-containing protein 12;
FUNCTION: Regulatory subunit that interacts with and increases the activity of different structure-specific endonucleases. Has several distinct roles in protecting genome stability by resolving diverse forms of deleterious DNA structures originating from replication and recombination intermediates and from DNA damage. Component of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products. Interacts with the structure- specific ERCC4-ERCC1 endonuclease and promotes the cleavage of bubble structures. Interacts with the structure-specific MUS81- EME1 endonuclease and promotes the cleavage of 3'-flap and replication fork-like structures. SLX4 is required for recovery from alkylation-induced DNA damage and is involved in the resolution of DNA double-strand breaks (By similarity).
SUBUNIT: Forms a heterodimer with SLX1A/GIYD1. Interacts with ERCC4; catalytic subunit of the ERCC4-ERCC1 endonuclease. Interacts with MUS81; catalytic subunit of the MUS81-EME1 endonuclease. Interacts with MSH2; component of the MSH2-MSH3 mismatch repair complex. Interacts with TERF2-TERF2IP. Interacts with PLK1 and C20ORF94 (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity). Note=Localizes to sites of DNA dammage (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the SLX4 family.
SIMILARITY: Contains 1 BTB (POZ) domain.

-  Primer design for this transcript
 

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-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -82.10310-0.265 Picture PostScript Text
3' UTR -204.90698-0.294 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000210 - BTB/POZ-like
IPR011333 - BTB/POZ_fold
IPR013069 - BTB_POZ

Pfam Domains:
PF00651 - BTB/POZ domain
PF09494 - Slx4 endonuclease

SCOP Domains:
54695 - POZ domain
57667 - beta-beta-alpha zinc fingers

ModBase Predicted Comparative 3D Structure on Q6P1D7
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsembl   
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008047 enzyme activator activity
GO:0008821 crossover junction endodeoxyribonuclease activity
GO:0017108 5'-flap endonuclease activity
GO:0048257 3'-flap endonuclease activity

Biological Process:
GO:0000706 meiotic DNA double-strand break processing
GO:0000712 resolution of meiotic recombination intermediates
GO:0000724 double-strand break repair via homologous recombination
GO:0006260 DNA replication
GO:0006281 DNA repair
GO:0006289 nucleotide-excision repair
GO:0006310 DNA recombination
GO:0006974 cellular response to DNA damage stimulus
GO:0010792 DNA double-strand break processing involved in repair via single-strand annealing
GO:0036297 interstrand cross-link repair
GO:0043085 positive regulation of catalytic activity
GO:0061820 telomeric D-loop disassembly
GO:0072429 response to intra-S DNA damage checkpoint signaling
GO:0090656 t-circle formation
GO:1904357 negative regulation of telomere maintenance via telomere lengthening
GO:1904431 positive regulation of t-circle formation

Cellular Component:
GO:0000781 chromosome, telomeric region
GO:0000784 nuclear chromosome, telomeric region
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0030054 cell junction
GO:0033557 Slx1-Slx4 complex
GO:0048476 Holliday junction resolvase complex
GO:0070522 ERCC4-ERCC1 complex


-  Descriptions from all associated GenBank mRNAs
  BC082337 - Mus musculus BTB (POZ) domain containing 12, mRNA (cDNA clone IMAGE:30536895).
BC065125 - Mus musculus BTB (POZ) domain containing 12, mRNA (cDNA clone MGC:86176 IMAGE:30534878), complete cds.
AK173263 - Mus musculus mRNA for mKIAA1784 protein.
AK042952 - Mus musculus 7 days neonate cerebellum cDNA, RIKEN full-length enriched library, clone:A730042P03 product:weakly similar to KIAA1784 PROTEIN (FRAGMENT) [Homo sapiens], full insert sequence.
AK041127 - Mus musculus adult male aorta and vein cDNA, RIKEN full-length enriched library, clone:A530084G07 product:hypothetical protein, full insert sequence.
BC042798 - Mus musculus BTB (POZ) domain containing 12, mRNA (cDNA clone IMAGE:4502463), partial cds.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q6P1D7 (Reactome details) participates in the following event(s):

R-MMU-5686475 SLX1A:SLX4 binds MUS81:EME1,(MUS81:EME2)
R-MMU-6785732 DNA nucleases bind monoubiquitinated ID2 complex
R-MMU-5693584 Cleavage of Holliday junctions by GEN1 or SLX1A:SLX4:MUS81:EME1,(MUS81:EME2)
R-MMU-5693568 Resolution of D-loop Structures through Holliday Junction Intermediates
R-MMU-6783310 Fanconi Anemia Pathway
R-MMU-5693537 Resolution of D-Loop Structures
R-MMU-73894 DNA Repair
R-MMU-5685942 HDR through Homologous Recombination (HRR)
R-MMU-5693567 HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
R-MMU-5693538 Homology Directed Repair
R-MMU-5693532 DNA Double-Strand Break Repair

-  Other Names for This Gene
  Alternate Gene Symbols: Btbd12, NM_177472, Q6P1D7, SLX4_MOUSE, uc007xzg.1, uc007xzg.2, uc007xzg.3, uc007xzg.4
UCSC ID: uc007xzg.4
RefSeq Accession: NM_177472
Protein: Q6P1D7 (aka SLX4_MOUSE)
CCDS: CCDS37240.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.