U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    Slf2 SMC5-SMC6 complex localization factor 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 499360, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Slf2provided by RGD
    Official Full Name
    SMC5-SMC6 complex localization factor 2provided by RGD
    Primary source
    RGD:1560300
    See related
    EnsemblRapid:ENSRNOG00000014482 AllianceGenome:RGD:1560300
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Fam178a; RGD1560300
    Summary
    Predicted to enable ubiquitin protein ligase binding activity. Predicted to be involved in several processes, including positive regulation of cellular component organization; positive regulation of double-strand break repair; and protein localization to site of double-strand break. Predicted to be located in PML body and chromatin. Predicted to be active in nucleus and site of double-strand break. Human ortholog(s) of this gene implicated in mosaic variegated aneuploidy syndrome. Orthologous to human SLF2 (SMC5-SMC6 complex localization factor 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 130.9), Brain (RPKM 115.7) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Slf2 in Genome Data Viewer
    Location:
    1q54
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (253731979..253794577)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (243782786..243845418)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (264670836..264733465)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120100041 Neighboring gene 5S ribosomal RNA Neighboring gene RNA, U6 small nuclear 588 Neighboring gene large ribosomal subunit protein eL21-like Neighboring gene semaphorin 4G Neighboring gene mitochondrial ribosomal protein L43 Neighboring gene twinkle mtDNA helicase

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. Alabert C, et al. Nat Cell Biol, 2014 Mar. PMID 24561620, 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. Comparison of tear protein levels in breast cancer patients and healthy controls using a de novo proteomic approach. Böhm D, et al. Oncol Rep, 2012 Aug. PMID 22664934, Free PMC Article
    4. 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

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin protein ligase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA damage response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of double-strand break repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of double-strand break repair 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
    		  
    involved_in positive regulation of protein-containing complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization to site of double-strand break IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein localization to site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in PML body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle 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
    		  
    located_in nucleus 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

    Go to the top of the page Help
    Preferred Names
    SMC5-SMC6 complex localization factor protein 2
    Names
    family with sequence similarity 178, member A
    protein FAM178A

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001134612.2 → NP_001128084.1  SMC5-SMC6 complex localization factor protein 2

      See identical proteins and their annotated locations for NP_001128084.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A6JHG9, D3ZF72
      Related
      ENSRNOP00000031171.4, ENSRNOT00000034814.8
      Conserved Domains (1) summary
      pfam14816
      Location:652 → 1018
      FAM178; Family of unknown function, FAM178

    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
      253731979..253794577
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017589590.3 → XP_017445079.1  SMC5-SMC6 complex localization factor protein 2 isoform X3

    2. XM_039088080.2 → XP_038944008.1  SMC5-SMC6 complex localization factor protein 2 isoform X4

      Conserved Domains (1) summary
      pfam14816
      Location:652 → 1003
      FAM178; Family of unknown function, FAM178

    3. XM_063271766.1 → XP_063127836.1  SMC5-SMC6 complex localization factor protein 2 isoform X5

    4. XM_006231550.5 → XP_006231612.1  SMC5-SMC6 complex localization factor protein 2 isoform X1

      Related
      ENSRNOP00000069230.3, ENSRNOT00000082412.3
      Conserved Domains (1) summary
      pfam14816
      Location:652 → 1019
      FAM178; Family of unknown function, FAM178

    5. XM_006231551.5 → XP_006231613.1  SMC5-SMC6 complex localization factor protein 2 isoform X2

      UniProtKB/TrEMBL
      A0A0G2JUU2
      Conserved Domains (1) summary
      pfam14816
      Location:652 → 1018
      FAM178; Family of unknown function, FAM178

    6. XM_039088085.2 → XP_038944013.1  SMC5-SMC6 complex localization factor protein 2 isoform X6

      UniProtKB/TrEMBL
      A0A0G2JUU2
      Conserved Domains (1) summary
      pfam14816
      Location:7 → 377
      FAM178; Family of unknown function, FAM178
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials
    Tools