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    Smc6 structural maintenance of chromosomes 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313961, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Smc6provided by RGD
    Official Full Name
    structural maintenance of chromosomes 6provided by RGD
    Primary source
    RGD:1311214
    See related
    EnsemblRapid:ENSRNOG00000004908 AllianceGenome:RGD:1311214
    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
    Smc6l1
    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. Predicted to be located in chromosome; mitotic spindle pole; and nuclear body. Predicted to be part of Smc5-Smc6 complex. Predicted to be active in nucleus and site of double-strand break. Orthologous to human SMC6 (structural maintenance of chromosomes 6). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 282.4), Testes (RPKM 237.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Smc6 in Genome Data Viewer
    Location:
    6q15
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (39697810..39752275)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (33978730..34033201)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (36941233..36995920)

    Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene mesogenin 1 Neighboring gene uncharacterized LOC102547959 Neighboring gene GEN1 Holliday junction 5' flap endonuclease Neighboring gene visinin-like 1 Neighboring gene mitochondrial ribosomal protein S10, pseudogene 1

    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. 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
    2. 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
    3. Identification of the proteins, including MAGEG1, that make up the human SMC5-6 protein complex. Taylor EM, et al. Mol Cell Biol, 2008 Feb. PMID 18086888, Free PMC Article
    4. The SMC5/6 complex maintains telomere length in ALT cancer cells through SUMOylation of telomere-binding proteins. Potts PR, et al. Nat Struct Mol Biol, 2007 Jul. PMID 17589526
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    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 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 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 cellular senescence 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 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 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 chromosome, centromeric region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromosome, telomeric region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in interchromatin granule ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitotic spindle pole ISO
    Inferred from Sequence Orthology
    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
    		  
    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
    		  
    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
    		  

    General protein information

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    Preferred Names
    structural maintenance of chromosomes protein 6
    Names
    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)

    1. NM_001108014.1 → NP_001101484.1  structural maintenance of chromosomes protein 6

      See identical proteins and their annotated locations for NP_001101484.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473947
      UniProtKB/TrEMBL
      A0A0G2JXU6, A6HAP6, D4AB26
      Related
      ENSRNOP00000007073.4, ENSRNOT00000007073.7
      Conserved Domains (1) summary
      COG1196
      Location:54 → 1075
      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_086024.1 Reference GRCr8

      Range
      39697810..39752275
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039112188.2 → XP_038968116.1  structural maintenance of chromosomes protein 6 isoform X1

      UniProtKB/TrEMBL
      A0A0G2JXU6, A6HAP6, D4AB26
      Related
      ENSRNOP00000078251.2, ENSRNOT00000110833.2
      Conserved Domains (1) summary
      COG1196
      Location:54 → 1075
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

    2. XM_006239898.5 → XP_006239960.1  structural maintenance of chromosomes protein 6 isoform X1

      See identical proteins and their annotated locations for XP_006239960.1

      UniProtKB/TrEMBL
      A0A0G2JXU6, A6HAP6, D4AB26
      Conserved Domains (1) summary
      COG1196
      Location:54 → 1075
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

    3. XM_039112189.2 → XP_038968117.1  structural maintenance of chromosomes protein 6 isoform X2

      UniProtKB/TrEMBL
      A0A0G2JXU6
      Conserved Domains (2) summary
      COG1196
      Location:20 → 877
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cl38936
      Location:785 → 883
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    4. XM_039112191.2 → XP_038968119.1  structural maintenance of chromosomes protein 6 isoform X3

      Conserved Domains (2) summary
      COG1196
      Location:9 → 723
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cl38936
      Location:631 → 729
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    5. XM_039112190.2 → XP_038968118.1  structural maintenance of chromosomes protein 6 isoform X3

      Conserved Domains (2) summary
      COG1196
      Location:9 → 723
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cl38936
      Location:631 → 729
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
    Nucleotide Protein Strain
    Heading Accession and Version

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