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    Safb scaffold attachment factor B [ Mus musculus (house mouse) ]

    Gene ID: 224903, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Safbprovided by MGI
    Official Full Name
    scaffold attachment factor Bprovided by MGI
    Primary source
    MGI:MGI:2146974
    See related
    Ensembl:ENSMUSG00000071054 AllianceGenome:MGI:2146974
    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
    HAP; HET; SAFB1; SAF-B1; E130307D12; 3110021E02Rik; 5330423C17Rik
    Summary
    Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and chromatin binding activity. Involved in positive regulation of transcription by RNA polymerase II. Acts upstream of or within estrogen receptor signaling pathway; hormone metabolic process; and regulation of growth. Predicted to be located in midbody and nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; future brain; olfactory epithelium; reproductive system; and retina layer. Orthologous to human SAFB (scaffold attachment factor B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 64.7), CNS E14 (RPKM 34.2) and 28 other tissues See more
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    Genomic context

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    See Safb in Genome Data Viewer
    Location:
    17 D; 17 29.4 cM
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (56891982..56913294)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (56584982..56606294)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene TINCR ubiquitin domain containing Neighboring gene scaffold attachment factor B2 Neighboring gene STARR-positive B cell enhancer ABC_E5623 Neighboring gene STARR-positive B cell enhancer ABC_E8687 Neighboring gene mitochondrial contact site and cristae organizing system subunit 13 Neighboring gene ribosomal protein L36

    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. SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells. Cherney RE, et al. RNA, 2023 Oct. PMID 37468167, Free PMC Article
    2. Scaffold attachment factor B1 directly interacts with nuclear receptors in living cells and represses transcriptional activity. Debril MB, et al. J Mol Endocrinol, 2005 Dec. PMID 16326836
    3. Scaffold Attachment Factor B1 (SAFB1) heterozygosity does not influence Wnt-1 or DMBA-induced tumorigenesis. Kaipparettu BA, et al. Mol Cancer, 2009 Mar 6. PMID 19267898, Free PMC Article
    4. The Werner syndrome helicase protein is required for cell proliferation, immortalization, and tumorigenesis in Scaffold attachment factor B1 deficient mice. Lachapelle S, et al. Aging (Albany NY), 2011 Mar. PMID 21464516, Free PMC Article
    5. Disruption of scaffold attachment factor B1 leads to TBX2 up-regulation, lack of p19ARF induction, lack of senescence, and cell immortalization. Dobrzycka KM, et al. Cancer Res, 2006 Aug 15. PMID 16912158

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SAFB regulates hippocampal stem cell fate by targeting Drosha to destabilize Nfib mRNA.
      Title: SAFB regulates hippocampal stem cell fate by targeting Drosha to destabilize Nfib mRNA.
    2. SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells.
      Title: SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells.
    3. despite a high degree of sequence similarity, SAFB1(-/-) and SAFB2(-/-) mice do not totally phenocopy each other
      Title: Scaffold attachment factor B2 (SAFB2)-null mice reveal non-redundant functions of SAFB2 compared with its paralog, SAFB1.
    4. Mice lacking SAFB1 exhibit developmental abnormalities in their lungs, high incidence of perinatal lethality, and adults develop different types of tumors. Mouse embryonic fibroblasts from Safb1-null animals are immortalized in culture.
      Title: The Werner syndrome helicase protein is required for cell proliferation, immortalization, and tumorigenesis in Scaffold attachment factor B1 deficient mice.
    5. Our data show that SAFB1 heterozygosity does not influence Wnt-1 induced tumorigenesis
      Title: Scaffold Attachment Factor B1 (SAFB1) heterozygosity does not influence Wnt-1 or DMBA-induced tumorigenesis.
    6. These results indicate a major role for SAFB1 in the activation of Srebp-1c through its interaction with RBMX.
      Title: SAFB1, an RBMX-binding protein, is a newly identified regulator of hepatic SREBP-1c gene.
    7. SAFB1 loss causes lack of contact inhibition, increased foci formation, and increased oncogene-induced anchorage-independent growth.
      Title: Disruption of scaffold attachment factor B1 leads to TBX2 up-regulation, lack of p19ARF induction, lack of senescence, and cell immortalization.
    8. SAFB1 plays a critical role in development, growth regulation, and reproduction.
      Title: Scaffold attachment factor B1 functions in development, growth, and reproduction.
    9. SAFB1 interacts in pull-down assays not only with PPARgamma but also with all nuclear receptors tested
      Title: Scaffold attachment factor B1 directly interacts with nuclear receptors in living cells and represses transcriptional activity.
    10. SAFB1 represses ERalpha activity via indirect association with histone deacetylation and interaction with the basal transcription machinery
      Title: Structure-function analysis of the estrogen receptor alpha corepressor scaffold attachment factor-B1: identification of a potent transcriptional repression domain.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (1)  1 citation

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in estrogen receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within estrogen receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within hormone metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of androgen receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of mRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of mRNA processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in midbody 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
    		  

    General protein information

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    Preferred Names
    scaffold attachment factor B1

    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_001163300.1 → NP_001156772.1  scaffold attachment factor B1 isoform 2

      See identical proteins and their annotated locations for NP_001156772.1

      Status: VALIDATED

      Source sequence(s)
      CT485788
      Consensus CDS
      CCDS50152.1
      UniProtKB/Swiss-Prot
      D3YXK2
      Related
      ENSMUSP00000092849.4, ENSMUST00000095224.11
      Conserved Domains (4) summary
      smart00513
      Location:31 → 65
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      PLN03124
      Location:32 → 183
      PLN03124; poly [ADP-ribose] polymerase; Provisional
      COG0724
      Location:368 → 527
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12679
      Location:427 → 502
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

    2. NM_001374619.1 → NP_001361548.1  scaffold attachment factor B1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      CT485788
      UniProtKB/TrEMBL
      S4R1M2
      Related
      ENSMUSP00000138277.2, ENSMUST00000182533.8
      Conserved Domains (4) summary
      smart00513
      Location:31 → 65
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      PLN03124
      Location:32 → 183
      PLN03124; poly [ADP-ribose] polymerase; Provisional
      COG0724
      Location:368 → 527
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12679
      Location:427 → 502
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

    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_000083.7 Reference GRCm39 C57BL/6J

      Range
      56891982..56913294
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017317445.1 → XP_017172934.1  scaffold attachment factor B1 isoform X1

      Conserved Domains (2) summary
      COG0724
      Location:211 → 370
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:270 → 345
      RRM_SF; RNA recognition motif (RRM) superfamily
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    D3YXK2.2 GenPept UniProtKB/Swiss-Prot:D3YXK2

    Gene LinkOut

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

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