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

    Gene ID: 293967, updated on 14-Nov-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 DNA secondary structure binding activity and single-stranded DNA binding activity. Predicted to be involved in several processes, including DNA recombination; negative regulation by host of viral genome replication; and positive regulation of cell cycle process. Predicted to act upstream of or within several processes, including internal peptidyl-lysine acetylation; mitotic cell cycle phase transition; 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. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in mosaic variegated aneuploidy syndrome. Orthologous to human SMC5 (structural maintenance of chromosomes 5). [provided by Alliance of Genome Resources, Nov 2024]
    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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    See Smc5 in Genome Data Viewer
    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
    • 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 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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