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Smc5 structural maintenance of chromosomes 5 [ Mus musculus (house mouse) ]

Gene ID: 226026, updated on 17-Aug-2024

Summary

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Official Symbol
Smc5provided by MGI
Official Full Name
structural maintenance of chromosomes 5provided by MGI
Primary source
MGI:MGI:2385088
See related
Ensembl:ENSMUSG00000024943 AllianceGenome:MGI:2385088
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-5; mSMC5; Smc5l1; MLZ-453; mKIAA0594
Summary
Predicted to enable ATP binding activity and ATP hydrolysis activity. Acts upstream of or within several processes, including chromosome condensation; internal peptidyl-lysine acetylation; and protein localization to chromosome, centromeric region. Located in PML body; chromosome; and cytoplasm. Part of Smc5-Smc6 complex. Is expressed in ovary; secondary spermatocyte; and testis. Orthologous to human SMC5 (structural maintenance of chromosomes 5). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in CNS E11.5 (RPKM 12.7), CNS E14 (RPKM 8.0) and 17 other tissues See more
Orthologs
human all
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Genomic context

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Location:
19 B; 19 18.04 cM
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (23183817..23251286, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (23206441..23273922, complement)

Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 2410080I02 gene Neighboring gene STARR-positive B cell enhancer ABC_E4273 Neighboring gene STARR-seq mESC enhancer starr_45766 Neighboring gene STARR-seq mESC enhancer starr_45769 Neighboring gene microRNA 1192 Neighboring gene Kruppel-like transcription factor 9 Neighboring gene STARR-seq mESC enhancer starr_45772 Neighboring gene STARR-positive B cell enhancer mm9_chr19:23348377-23348678 Neighboring gene predicted gene, 33950 Neighboring gene predicted gene, 24263 Neighboring gene predicted gene, 41821 Neighboring gene MAM domain containing 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data 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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Related articles in PubMed

  1. Conditional Mutation of SMC5 in Mouse Embryonic Fibroblasts. Gaddipati H, et al. Methods Mol Biol, 2019. PMID 31147908, Free PMC Article
  2. Depletion of SMC5/6 sensitizes male germ cells to DNA damage. Hwang G, et al. Mol Biol Cell, 2018 Dec 1. PMID 30281394, Free PMC Article
  3. Telomeric DNA mediates de novo PML body formation. Brouwer AK, et al. Mol Biol Cell, 2009 Nov. PMID 19793919, Free PMC Article
  4. Characterization of a novel human SMC heterodimer homologous to the Schizosaccharomyces pombe Rad18/Spr18 complex. Taylor EM, et al. Mol Biol Cell, 2001 Jun. PMID 11408570, Free PMC Article
  5. Conditional mutation of Smc5 in mouse embryonic stem cells perturbs condensin localization and mitotic progression. Pryzhkova MV, et al. J Cell Sci, 2016 Apr 15. PMID 26919979, Free PMC Article

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. Study the function and properties of the SMC5/6 complex in mammals.
    Title: Conditional Mutation of SMC5 in Mouse Embryonic Fibroblasts.
  4. 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.
Submit: New GeneRIF Correction

Variation

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Alleles

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC7569, MGC30442

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 molecular_function ND
No biological Data available
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
  
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 DNA repair IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cell cycle IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular senescence ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within chromosome condensation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within chromosome segregation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in double-strand break repair via homologous recombination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in double-strand break repair via homologous recombination ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within internal peptidyl-lysine acetylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within mitotic cell cycle phase transition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 maintenance of mitotic sister chromatid cohesion ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within protein localization to chromosome, centromeric region IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in telomere maintenance via recombination ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in PML body IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in PML body ISO
Inferred from Sequence Orthology
more info
  
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 cell junction 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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in chromosome, telomeric region ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in interchromatin granule ISO
Inferred from Sequence Orthology
more info
  
located_in nuclear speck 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 
located_in site of double-strand break ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
structural maintenance of chromosomes protein 5
Names
SMC protein 5
SMC5 structural maintenance of chromosomes 5-like 1
protein expressed in male leptotene and zygotene spermatocytes 453

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_001252684.2 → NP_001239613.1  structural maintenance of chromosomes protein 5 isoform 1

    See identical proteins and their annotated locations for NP_001239613.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC144941
    Consensus CDS
    CCDS89364.1
    UniProtKB/Swiss-Prot
    Q80TW7, Q8CG46, Q8CHX5, Q922K3
    Related
    ENSMUSP00000084837.7, ENSMUST00000087556.7
    Conserved Domains (2) summary
    cd03277
    Location:975 → 1077
    ABC_SMC5_euk; ATP-binding cassette domain of eukaryotic SMC5 proteins
    COG1196
    Location:53 → 1055
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

  2. NM_001252685.2 → NP_001239614.1  structural maintenance of chromosomes protein 5 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, initiates translation at a downstream, in-frame start codon and lacks an exon in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC144941
    Consensus CDS
    CCDS89363.1
    UniProtKB/TrEMBL
    A0A286YDG5
    Related
    ENSMUSP00000153420.2, ENSMUST00000226111.2
    Conserved Domains (2) summary
    cd03277
    Location:885 → 987
    ABC_SMC5_euk; ATP-binding cassette domain of eukaryotic SMC5 proteins
    COG1196
    Location:1 → 965
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

  3. NM_001426152.1 → NP_001413081.1  structural maintenance of chromosomes protein 5 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC144941

  4. NM_001426153.1 → NP_001413082.1  structural maintenance of chromosomes protein 5 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC144941

  5. NM_153808.3 → NP_722503.1  structural maintenance of chromosomes protein 5 isoform 2

    See identical proteins and their annotated locations for NP_722503.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC144941
    Consensus CDS
    CCDS37936.1
    UniProtKB/Swiss-Prot
    Q8CG46
    Related
    ENSMUSP00000153364.2, ENSMUST00000223934.2
    Conserved Domains (2) summary
    cd03277
    Location:961 → 1063
    ABC_SMC5_euk; ATP-binding cassette domain of eukaryotic SMC5 proteins
    COG1196
    Location:53 → 1041
    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_000085.7 Reference GRCm39 C57BL/6J

    Range
    23183817..23251286 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001782581.2 RNA Sequence

  2. XR_003952782.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8CG46.1 GenPept UniProtKB/Swiss-Prot:Q8CG46

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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