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    Slf2 SMC5-SMC6 complex localization factor 2 [ Mus musculus (house mouse) ]

    Gene ID: 226151, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Slf2provided by MGI
    Official Full Name
    SMC5-SMC6 complex localization factor 2provided by MGI
    Primary source
    MGI:MGI:1924968
    See related
    Ensembl:ENSMUSG00000036097 AllianceGenome:MGI:1924968
    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
    Fam178a; 3632432H19
    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, Nov 2024]
    Expression
    Ubiquitous expression in CNS E18 (RPKM 11.0), ovary adult (RPKM 9.6) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Slf2 in Genome Data Viewer
    Location:
    19 C3; 19 38.16 cM
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (44906948..44972225)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (44918506..44983786)

    Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene paired box 2 Neighboring gene RIKEN cDNA 1700039E22 gene Neighboring gene STARR-seq mESC enhancer starr_46250 Neighboring gene STARR-seq mESC enhancer starr_46251 Neighboring gene 3-phosphoglycerate dehydrogenase pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E1526 Neighboring gene STARR-positive B cell enhancer ABC_E11031 Neighboring gene predicted gene, 25482 Neighboring gene RIKEN cDNA 4930414N06 gene Neighboring gene STARR-positive B cell enhancer ABC_E9998 Neighboring gene sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G Neighboring gene mitochondrial ribosomal protein L43 Neighboring gene twinkle mtDNA helicase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article
    2. A large-scale, gene-driven mutagenesis approach for the functional analysis of the mouse genome. Hansen J, et al. Proc Natl Acad Sci U S A, 2003 Aug 19. PMID 12904583, Free PMC Article
    3. Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Ko MS, et al. Development, 2000 Apr. PMID 10725249
    4. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Stryke D, et al. Nucleic Acids Res, 2003 Jan 1. PMID 12520002, Free PMC Article
    5. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Pourhaghighi R, et al. Cell Syst, 2020 Apr 22. PMID 32325033, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • 6030443O07Rik

    Gene Ontology Provided by MGI

    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 DNA damage response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    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 double-strand break repair ISS
    Inferred from Sequence or Structural Similarity
    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 maintenance of mitotic sister chromatid cohesion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of protein-containing complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of protein-containing complex assembly ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    involved_in protein localization to site of double-strand break ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in PML body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in PML body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatin ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    located_in site of double-strand break ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    SMC5-SMC6 complex localization factor protein 2
    Names
    family with sequence similarity 178, member A
    protein FAM178A

    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_001081225.3 → NP_001074694.1  SMC5-SMC6 complex localization factor protein 2 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC131105, AC132957
      Consensus CDS
      CCDS37999.1
      UniProtKB/TrEMBL
      B2RXQ3, E9Q839
      Related
      ENSMUSP00000093758.4, ENSMUST00000096053.6
      Conserved Domains (1) summary
      pfam14816
      Location:652 → 1018
      FAM178; Family of unknown function, FAM178

    RNA

    1. NR_175948.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC131105, AC132957

    2. NR_175949.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC131105, AC132957

    3. NR_175983.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC131105, AC132957
      Related
      ENSMUST00000236895.2

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000085.7 Reference GRCm39 C57BL/6J

      Range
      44906948..44972225
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006527000.5 → XP_006527063.1  SMC5-SMC6 complex localization factor protein 2 isoform X1

      UniProtKB/TrEMBL
      B2RXQ3
      Conserved Domains (2) summary
      PTZ00108
      Location:270 → 550
      PTZ00108; DNA topoisomerase 2-like protein; Provisional
      pfam14816
      Location:588 → 957
      FAM178; Family of unknown function, FAM178

    2. XM_011247236.4 → XP_011245538.1  SMC5-SMC6 complex localization factor protein 2 isoform X2

      UniProtKB/TrEMBL
      Q3UH46
      Conserved Domains (2) summary
      PTZ00108
      Location:334 → 614
      PTZ00108; DNA topoisomerase 2-like protein; Provisional
      pfam14816
      Location:652 → 731
      FAM178; Family of unknown function, FAM178

    RNA

    1. XR_001782585.2 RNA Sequence

    2. XR_004940142.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_172638.3: Suppressed sequence

      Description
      NM_172638.3: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6P9P0.2 GenPept UniProtKB/Swiss-Prot:Q6P9P0

    Gene LinkOut

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

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