Mouse Gene Smc6 (ENSMUST00000218866.1) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Core component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via recombination and mediates sumoylation of shelterin complex (telosome) components (By similarity). (from UniProt Q924W5)
Gencode Transcript: ENSMUST00000218866.1
Gencode Gene: ENSMUSG00000020608.7
Transcript (Including UTRs)
   Position: mm10 chr12:11,266,129-11,287,654 Size: 21,526 Total Exon Count: 10 Strand: +
Coding Region
   Position: mm10 chr12:11,271,734-11,285,427 Size: 13,694 Coding Exon Count: 9 

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 (chr12:11,266,129-11,287,654)mRNA (may differ from genome)Protein (326 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsMGIPubMed
ReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SMC6_MOUSE
DESCRIPTION: RecName: Full=Structural maintenance of chromosomes protein 6; Short=SMC protein 6; Short=SMC-6; Short=mSMC6;
FUNCTION: Core component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via recombination and mediates sumoylation of shelterin complex (telosome) components (By similarity).
SUBUNIT: Forms a heterodimer with SMC5. Component of the SMC5-SMC6 complex which consists at least of SMC5, SMC6, NSMCE2, NSMCE1, NSMCE4A or EID3 and NDNL2 (By similarity).
SUBCELLULAR LOCATION: Nucleus. Chromosome. Chromosome, telomere (By similarity). Note=Associates with chromatin.
DOMAIN: The flexible hinge domain, which separates the large intramolecular coiled coil regions, allows the heterotypic interaction with the corresponding domain of SMC5, forming a V- shaped heterodimer (By similarity).
PTM: Phosphorylated (By similarity).
PTM: Sumoylated by NSMCE2/MMS21 (By similarity).
PTM: Ubiquitinated (By similarity).
SIMILARITY: Belongs to the SMC family. SMC6 subfamily.
SEQUENCE CAUTION: Sequence=BAB23051.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -88.60165-0.537 Picture PostScript Text
3' UTR -539.202227-0.242 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
IPR003395 - RecF/RecN/SMC

Pfam Domains:
PF02463 - RecF/RecN/SMC N terminal domain
PF13476 - AAA domain

SCOP Domains:
69179 - Integrin domains
52540 - P-loop containing nucleoside triphosphate hydrolases
58100 - Bacterial hemolysins

ModBase Predicted Comparative 3D Structure on Q924W5
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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     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005524 ATP binding
GO:0031625 ubiquitin protein ligase binding

Biological Process:
GO:0000722 telomere maintenance via recombination
GO:0000724 double-strand break repair via homologous recombination
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0006974 cellular response to DNA damage stimulus
GO:0051984 positive regulation of chromosome segregation
GO:0090398 cellular senescence

Cellular Component:
GO:0000781 chromosome, telomeric region
GO:0000803 sex chromosome
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0016605 PML body
GO:0016607 nuclear speck
GO:0030915 Smc5-Smc6 complex
GO:0035061 interchromatin granule
GO:0035861 site of double-strand break


-  Descriptions from all associated GenBank mRNAs
  BC090630 - Mus musculus structural maintenance of chromosomes 6, mRNA (cDNA clone MGC:96146 IMAGE:30536320), complete cds.
AK220488 - Mus musculus mRNA for mKIAA4103 protein.
AK148478 - Mus musculus adult pancreas islet cells cDNA, RIKEN full-length enriched library, clone:C820008H24 product:SMC6 structural maintenance of chromosomes 6-like 1 (yeast), full insert sequence.
AK012626 - Mus musculus 10, 11 days embryo whole body cDNA, RIKEN full-length enriched library, clone:2810001A05 product:RIKEN cDNA 2810489L22 gene, full insert sequence.
BC048790 - Mus musculus structural maintenance of chromosomes 6, mRNA (cDNA clone IMAGE:6308536), complete cds.
AK088002 - Mus musculus 2 days neonate thymus thymic cells cDNA, RIKEN full-length enriched library, clone:E430002B08 product:RIKEN cDNA 2810489L22 gene, full insert sequence.
AK135873 - Mus musculus in vitro fertilized eggs cDNA, RIKEN full-length enriched library, clone:7420431F11 product:SMC6 structural maintenance of chromosomes 6-like 1 (yeast), full insert sequence.
AK009009 - Mus musculus adult male tongue cDNA, RIKEN full-length enriched library, clone:2300002F20 product:RIKEN cDNA 2810489L22 gene, full insert sequence.
AK011982 - Mus musculus 10 days embryo whole body cDNA, RIKEN full-length enriched library, clone:2610304I02 product:hypothetical SMC domain N terminal domain containing protein, full insert sequence.
AK050341 - Mus musculus adult male liver tumor cDNA, RIKEN full-length enriched library, clone:C730038K07 product:SMC6 PROTEIN, full insert sequence.
BC099955 - Mus musculus structural maintenance of chromosomes 6, mRNA (cDNA clone IMAGE:30052739), partial cds.
AJ310552 - Mus musculus mRNA for SMC6 protein.
AK019823 - Mus musculus adult male testis cDNA, RIKEN full-length enriched library, clone:4930580I18 product:SMC6 PROTEIN homolog [Mus musculus], full insert sequence.
AK201968 - Mus musculus cDNA, clone:Y1G0139P10, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000051716, based on BLAT search.

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

Protein Q924W5 (Reactome details) participates in the following event(s):

R-MMU-3108212 SMC5-SMC6 Complex SUMOylates Cohesin with SUMO1
R-MMU-3108214 SUMOylation of DNA damage response and repair proteins
R-MMU-3108232 SUMO E3 ligases SUMOylate target proteins
R-MMU-2990846 SUMOylation
R-MMU-597592 Post-translational protein modification
R-MMU-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: BC048790, Kiaa4103, Q3UFI5, Q3UX54, Q499E1, Q5DTN2, Q8BFU9, Q8R0T4, Q924W5, Q9CSK7, Q9CV94, Q9CZZ5, Q9D169, Q9D6B2, Smc6l1, SMC6_MOUSE, uc007nax.1, uc007nax.2
UCSC ID: uc007nax.2
RefSeq Accession: NM_001361252
Protein: Q924W5 (aka SMC6_MOUSE)

-  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.