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

Gene ID: 224903, updated on 14-Nov-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, Nov 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 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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