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

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 DNA binding activity and ubiquitin protein ligase binding activity. Predicted to be involved in several processes, including DNA recombination; cellular senescence; and negative regulation by host of viral genome replication. 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, Nov 2024]
Expression: Broad expression in CNS E11.5 (RPKM 10.6), placenta adult (RPKM 6.0) and 22 other tissues See more
Orthologs: human all
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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_000078.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

SMC5/6 is required for replication fork stability and faithful chromosome segregation during neurogenesis.
Title: SMC5/6 is required for replication fork stability and faithful chromosome segregation during neurogenesis.
SMC5/6 complex is essential only when meiotic DNA processing events are perturbed during mouse spermatogenesis
Title: Depletion of SMC5/6 sensitizes male germ cells to DNA damage.
age-dependent depletion of the SMC5/6 complex in oocytes could contribute to increased incidence of oocyte aneuploidy and spontaneous abortion in aging females.
Title: SMC5/6 is required for the formation of segregation-competent bivalent chromosomes during meiosis I in mouse oocytes.
Smc6 has a role in the prevention of aberrant recombination events between pericentromeric regions during the first meiotic prophase.
Title: Role for rodent Smc6 in pericentromeric heterochromatin domains during spermatogonial differentiation and meiosis.
Mice deleted for the SMC6 gene are inviable, and mice mutated at Ser-994 in the SMC6 ATPase domain have a mild phenotype.
Title: SMC6 is an essential gene in mice, but a hypomorphic mutant in the ATPase domain has a mild phenotype with a range of subtle abnormalities.

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Variation

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Alleles

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

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:236808

AA990493 (e-PCR)
- UniSTS:160849

AW742439 (e-PCR)
- UniSTS:208776

AU018782 (e-PCR)
- UniSTS:160182

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	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 single-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase binding	IEA Inferred from Electronic Annotation 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
involved_in DNA damage response	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular senescence	ISO Inferred from Sequence Orthology more info
involved_in cellular senescence	ISS Inferred from Sequence or Structural Similarity 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	IEA Inferred from Electronic Annotation 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 positive regulation of chromosome segregation	ISS Inferred from Sequence or Structural Similarity more info
involved_in telomere maintenance via recombination	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance via recombination	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in PML body	ISO Inferred from Sequence Orthology more info
located_in PML body	ISS Inferred from Sequence or Structural Similarity 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
part_of Smc5-Smc6 complex	ISS Inferred from Sequence or Structural Similarity 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	ISS Inferred from Sequence or Structural Similarity 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 interchromatin granule	ISS Inferred from Sequence or Structural Similarity more info
located_in mitotic spindle pole	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
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 nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity 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
located_in site of double-strand break	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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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)

NM_001324476.1 → NP_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:785 → 883

ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins

COG1196
Location:20 → 877

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
NM_001361252.1 → NP_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:54 → 210

ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins

cl25732
Location:54 → 319

SMC_N; RecF/RecN/SMC N terminal domain
NM_025695.4 → NP_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:983 → 1081

ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins

COG1196
Location:54 → 1075

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

NC_000078.7 Reference GRCm39 C57BL/6J

Range

11315887..11369786

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (2) summary

cd03276
Location:54 → 210

ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins

COG1196
Location:54 → 885

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
XM_006515173.4 → XP_006515236.1 structural maintenance of chromosomes protein 6 isoform X1

Conserved Domains (3) summary

cd03276
Location:895 → 993

ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins

COG1196
Location:130 → 987

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

cl38936
Location:34 → 122

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases