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Smc5 structural maintenance of chromosomes 5 [ Rattus norvegicus (Norway rat) ]

Gene ID: 293967, updated on 18-Sep-2024

Summary

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Official Symbol
Smc5provided by RGD
Official Full Name
structural maintenance of chromosomes 5provided by RGD
Primary source
RGD:1307492
See related
EnsemblRapid:ENSRNOG00000030572 AllianceGenome:RGD:1307492
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Smc5l1
Summary
Predicted to enable ATP binding activity. Predicted to be involved in several processes, including DNA recombination; cellular senescence; and positive regulation of maintenance of mitotic sister chromatid cohesion. Predicted to act upstream of or within several processes, including chromosome condensation; internal peptidyl-lysine acetylation; and protein localization to chromosome, centromeric region. Predicted to be located in several cellular components, including cell junction; chromosome; and nuclear body. Predicted to be part of Smc5-Smc6 complex. Orthologous to human SMC5 (structural maintenance of chromosomes 5). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Thymus (RPKM 136.7), Lung (RPKM 110.9) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
1q51
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (230195894..230265677, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (220769366..220839138, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (240977898..241046273, complement)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene 40S ribosomal protein S12-like Neighboring gene uncharacterized LOC108349100 Neighboring gene uncharacterized LOC134485213 Neighboring gene KLF transcription factor 9 Neighboring gene RNA, U6 small nuclear 806 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Telomeric DNA mediates de novo PML body formation. Brouwer AK, et al. Mol Biol Cell, 2009 Nov. PMID 19793919, Free PMC Article
  2. SMC5 and MMS21 are required for chromosome cohesion and mitotic progression. Behlke-Steinert S, et al. Cell Cycle, 2009 Jul 15. PMID 19502785
  3. 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
  4. DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links. Räschle M, et al. Science, 2015 May 1. PMID 25931565, Free PMC Article
  5. Human SMC5/6 complex promotes sister chromatid homologous recombination by recruiting the SMC1/3 cohesin complex to double-strand breaks. Potts PR, et al. EMBO J, 2006 Jul 26. PMID 16810316, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

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 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
  
involved_in cellular senescence ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within chromosome condensation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within chromosome segregation ISO
Inferred from Sequence Orthology
more info
  
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
  
NOT involved_in double-strand break repair via nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within internal peptidyl-lysine acetylation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within mitotic cell cycle phase transition ISO
Inferred from Sequence Orthology
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 maintenance of mitotic sister chromatid cohesion ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within protein localization to chromosome, centromeric region ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within stem cell population maintenance 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
  
part_of Smc5-Smc6 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
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, centromeric region ISO
Inferred from Sequence Orthology
more info
  
located_in chromosome, telomeric region ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
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
  
is_active_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in sex chromosome ISO
Inferred from Sequence Orthology
more info
  
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
SMC5 structural maintenance of chromosomes 5-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_001106357.2 → NP_001099827.1  structural maintenance of chromosomes protein 5

    See identical proteins and their annotated locations for NP_001099827.1

    Status: PROVISIONAL

    Source sequence(s)
    JAXUCZ010000001
    UniProtKB/TrEMBL
    A6I0N4, A6I0N5, D4A9F0
    Related
    ENSRNOP00000061357.1, ENSRNOT00000067796.4
    Conserved Domains (2) summary
    cd03277
    Location:937 → 1039
    ABC_SMC5_euk; ATP-binding cassette domain of eukaryotic SMC5 proteins
    COG1196
    Location:53 → 1017
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086019.1 Reference GRCr8

    Range
    230195894..230265677 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006231183.4 → XP_006231245.1  structural maintenance of chromosomes protein 5 isoform X1

    UniProtKB/TrEMBL
    A6I0N4
    Related
    ENSRNOP00000108756.1, ENSRNOT00000153031.1
    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. XM_006231184.4 → XP_006231246.1  structural maintenance of chromosomes protein 5 isoform X2

    UniProtKB/TrEMBL
    A0A0G2K4T5, A6I0N4
    Related
    ENSRNOP00000073164.2, ENSRNOT00000081866.3
    Conserved Domains (2) summary
    cd03277
    Location:960 → 1062
    ABC_SMC5_euk; ATP-binding cassette domain of eukaryotic SMC5 proteins
    COG1196
    Location:53 → 1040
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

  3. XM_063287099.1 → XP_063143169.1  structural maintenance of chromosomes protein 5 isoform X3

  4. XM_039108980.2 → XP_038964908.1  structural maintenance of chromosomes protein 5 isoform X4

    Conserved Domains (2) summary
    COG1196
    Location:53 → 456
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cl38936
    Location:51 → 196
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
Nucleotide Protein Strain
Heading Accession and Version

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