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

Summary

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

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_000085.7 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.
Study the function and properties of the SMC5/6 complex in mammals.
Title: Conditional Mutation of SMC5 in Mouse Embryonic Fibroblasts.
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)

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:237909

NoName (e-PCR)
- UniSTS:237911

D19Ertd756e (e-PCR), detects polymorphism
- UniSTS:167258

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)

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

Status: VALIDATED

Source sequence(s)

AC144941
NM_001426153.1 → NP_001413082.1 structural maintenance of chromosomes protein 5 isoform 5

Status: VALIDATED

Source sequence(s)

AC144941
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]