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

Gene ID: 226151, updated on 5-Mar-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 act upstream of or within DNA repair. Predicted to be located in chromatin and nucleoplasm. Predicted to be active in nucleus and site of double-strand break. Orthologous to human SLF2 (SMC5-SMC6 complex localization factor 2). [provided by Alliance of Genome Resources, Apr 2022]
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
  
acts_upstream_of_or_within 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 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
  
part_of 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

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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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