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Smc6 structural maintenance of chromosomes 6 [ Mus musculus (house mouse) ]

Gene ID: 67241, updated on 21-Apr-2024

Summary

Official Symbol
Smc6provided by MGI
Official Full Name
structural maintenance of chromosomes 6provided by MGI
Primary source
MGI:MGI:1914491
See related
Ensembl:ENSMUSG00000020608 AllianceGenome:MGI:1914491
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
SMC-6; Smc6l1; mKIAA4103; 2810489L22Rik; 3830418C19Rik
Summary
Predicted to enable damaged DNA binding activity; single-stranded DNA binding activity; and ubiquitin protein ligase binding activity. Predicted to be involved in DNA recombination; cellular senescence; and positive regulation of chromosome segregation. Predicted to act upstream of or within DNA recombination and DNA repair. Located in chromosome; mitotic spindle pole; and nucleus. Part of Smc5-Smc6 complex. Is expressed in central nervous system; embryo; retina; retina inner nuclear layer; and retina outer nuclear layer. Orthologous to human SMC6 (structural maintenance of chromosomes 6). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in CNS E11.5 (RPKM 10.6), placenta adult (RPKM 6.0) and 22 other tissues See more
Orthologs
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Genomic context

Location:
12 A1.1; 12 5.58 cM
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (11315887..11369786)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (11265886..11319785)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 9530020I12 gene Neighboring gene STARR-seq mESC enhancer starr_31537 Neighboring gene STARR-seq mESC enhancer starr_31538 Neighboring gene STARR-positive B cell enhancer ABC_E7120 Neighboring gene mesogenin 1 Neighboring gene STARR-positive B cell enhancer ABC_E8479 Neighboring gene GEN1, Holliday junction 5' flap endonuclease Neighboring gene STARR-seq mESC enhancer starr_31540 Neighboring gene microRNA 7675 Neighboring gene visinin-like 1 Neighboring gene STARR-seq mESC enhancer starr_31541 Neighboring gene RIKEN cDNA 4930511A02 gene

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)
  • Gene trapped (1) 
  • Targeted (4)  1 citation
  • Endonuclease-mediated (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • KIAA4103, MGC96146

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
 
enables DNA secondary structure binding ISO
Inferred from Sequence Orthology
more info
 
enables damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
enables single-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables ubiquitin protein ligase binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in DNA damage response ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within DNA recombination IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within DNA repair IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular senescence ISO
Inferred from Sequence Orthology
more info
 
involved_in double-strand break repair IEA
Inferred from Electronic Annotation
more info
 
involved_in double-strand break repair via homologous recombination IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation by host of viral genome replication ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of chromosome segregation ISO
Inferred from Sequence Orthology
more info
 
involved_in telomere maintenance via recombination ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in PML body ISO
Inferred from Sequence Orthology
more info
 
located_in PML body TAS
Traceable Author Statement
more info
PubMed 
part_of Smc5-Smc6 complex IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of Smc5-Smc6 complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of Smc5-Smc6 complex ISO
Inferred from Sequence Orthology
more info
 
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in chromosome, centromeric region IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromosome, telomeric region ISO
Inferred from Sequence Orthology
more info
 
located_in chromosome, telomeric region TAS
Traceable Author Statement
more info
PubMed 
located_in interchromatin granule ISO
Inferred from Sequence Orthology
more info
 
located_in mitotic spindle pole IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in sex chromosome IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in site of double-strand break IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in site of double-strand break ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
structural maintenance of chromosomes protein 6
Names
SMC protein 6
SMC6 structural maintenance of chromosomes 6-like 1

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_001324476.1NP_001311405.1  structural maintenance of chromosomes protein 6 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AK220488, BC090630
    UniProtKB/Swiss-Prot
    Q924W5
    Conserved Domains (2) summary
    cd03276
    Location:785883
    ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
    COG1196
    Location:20877
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
  2. NM_001361252.1NP_001348181.1  structural maintenance of chromosomes protein 6 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AK011982, BC090630
    Consensus CDS
    CCDS88313.1
    Related
    ENSMUSP00000151976.2, ENSMUST00000218866.2
    Conserved Domains (2) summary
    cd03276
    Location:54210
    ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
    cl25732
    Location:54319
    SMC_N; RecF/RecN/SMC N terminal domain
  3. NM_025695.4NP_079971.2  structural maintenance of chromosomes protein 6 isoform 1

    See identical proteins and their annotated locations for NP_079971.2

    Status: VALIDATED

    Source sequence(s)
    AC104880, AC139207
    Consensus CDS
    CCDS25815.1
    UniProtKB/Swiss-Prot
    Q3UFI5, Q3UX54, Q499E1, Q5DTN2, Q8BFU9, Q8R0T4, Q924W5, Q9CSK7, Q9CV94, Q9CZZ5, Q9D169, Q9D6B2
    Related
    ENSMUSP00000020931.6, ENSMUST00000020931.6
    Conserved Domains (2) summary
    cd03276
    Location:9831081
    ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
    COG1196
    Location:541075
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

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_000078.7 Reference GRCm39 C57BL/6J

    Range
    11315887..11369786
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011243892.4XP_011242194.1  structural maintenance of chromosomes protein 6 isoform X2

    Conserved Domains (2) summary
    cd03276
    Location:54210
    ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
    COG1196
    Location:54885
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
  2. XM_006515173.4XP_006515236.1  structural maintenance of chromosomes protein 6 isoform X1

    Conserved Domains (3) summary
    cd03276
    Location:895993
    ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
    COG1196
    Location:130987
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cl38936
    Location:34122
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases