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    SAFB2 scaffold attachment factor B2 [ Homo sapiens (human) ]

    Gene ID: 9667, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SAFB2provided by HGNC
    Official Full Name
    scaffold attachment factor B2provided by HGNC
    Primary source
    HGNC:HGNC:21605
    See related
    Ensembl:ENSG00000130254 MIM:608066; AllianceGenome:HGNC:21605
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    The protein encoded by this gene, along with its paralog (scaffold attachment factor B1), is a repressor of estrogen receptor alpha. The encoded protein binds scaffold/matrix attachment region (S/MAR) DNA and is involved in cell cycle regulation, apoptosis, differentiation, the stress response, and regulation of immune genes. [provided by RefSeq, May 2016]
    Expression
    Ubiquitous expression in kidney (RPKM 19.8), spleen (RPKM 18.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SAFB2 in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (5586999..5622776, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (5573679..5609458, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (5587010..5622787, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5560556-5561352 Neighboring gene TINCR ubiquitin domain containing Neighboring gene SNRPE pseudogene 4 Neighboring gene Sharpr-MPRA regulatory regions 733 and 12449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5589167-5589789 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:5611821-5613020 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5621326-5622058 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9924 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:5622792-5623524 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:5623525-5624256 Neighboring gene scaffold attachment factor B Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:5648485-5649684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5666846-5667760 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5667761-5668675 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5668838-5669338 Neighboring gene uncharacterized LOC107985320

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Scaffold attachment factors SAFB1 and SAFB2: Innocent bystanders or critical players in breast tumorigenesis? Oesterreich S. J Cell Biochem, 2003 Nov 1. PMID 14587024
    2. Unravelling the RNA-Binding Properties of SAFB Proteins in Breast Cancer Cells. Hong E, et al. Biomed Res Int, 2015. PMID 26273616, Free PMC Article
    3. SAFB2 Inhibits the Progression of Breast Cancer by Suppressing the Wnt/β-Catenin Signaling Pathway via NFAT5. Zhen H, et al. Mol Biotechnol, 2023 Sep. PMID 36652182
    4. Scaffold attachment factor B (SAFB)1 and SAFB2 cooperatively inhibit the intranuclear mobility and function of ERα. Hashimoto T, et al. J Cell Biochem, 2012 Sep. PMID 22566185
    5. No germline mutations in supposed tumour suppressor genes SAFB1 and SAFB2 in familial breast cancer with linkage to 19p. Bergman A, et al. BMC Med Genet, 2008 Dec 13. PMID 19077293, Free PMC Article

    See all (122) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SAFB2 Inhibits the Progression of Breast Cancer by Suppressing the Wnt/beta-Catenin Signaling Pathway via NFAT5.
      Title: SAFB2 Inhibits the Progression of Breast Cancer by Suppressing the Wnt/β-Catenin Signaling Pathway via NFAT5.
    2. SAFB2 Enables the Processing of Suboptimal Stem-Loop Structures in Clustered Primary miRNA Transcripts.
      Title: SAFB2 Enables the Processing of Suboptimal Stem-Loop Structures in Clustered Primary miRNA Transcripts.
    3. Single depletion of either SAFB1 or SAFB2 leads to an increase in expression of the other SAFB protein.
      Title: Unravelling the RNA-Binding Properties of SAFB Proteins in Breast Cancer Cells.
    4. Results indicate that SAFB1 and SAFB2 are crucial repressors for ERalpha dynamics in association with the nuclear matrix and that their synergistic regulation of ERalpha mobility is sufficient for inhibiting ERalpha function.
      Title: Scaffold attachment factor B (SAFB)1 and SAFB2 cooperatively inhibit the intranuclear mobility and function of ERα.
    5. This study shows that low SAFB protein levels predict poor prognosis of breast cancer patients, suggesting critical functions of SAFB1 and SAFB2 in breast cancer cells.
      Title: Low SAFB levels are associated with worse outcome in breast cancer patients.
    6. Study confirms the primary role of SAFB1/SAFB2 as corepressors and also uncovers a previously unknown role for SAFB1 in the regulation of immune genes and in estrogen-mediated repression of genes.
      Title: SAFB1 mediates repression of immune regulators and apoptotic genes in breast cancer cells.
    7. The enzymatic activity of SR protein kinases 1 and 1a is negatively affected by interaction with scaffold attachment factors B1 and 2.
      Title: The enzymatic activity of SR protein kinases 1 and 1a is negatively affected by interaction with scaffold attachment factors B1 and 2.
    8. SAFB2 is not likely to be causative of the hereditary breast cancer syndrome in west Swedish breast cancer families
      Title: No germline mutations in supposed tumour suppressor genes SAFB1 and SAFB2 in familial breast cancer with linkage to 19p.
    9. REVIEW: possibility that SAFB1 and SAFB2 are novel breast tumor suppressor genes, and how they might function in this role, are discussed
      Title: Scaffold attachment factors SAFB1 and SAFB2: Innocent bystanders or critical players in breast tumorigenesis?
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Combined analysis of three genome-wide association studies on vWF and FVIII plasma levels.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0138

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    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
    		  
    Process Evidence Code Pubs
    involved_in Sertoli cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of androgen receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of mRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    scaffold attachment factor B2

    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.

    Genomic

    1. NG_050735.1 RefSeqGene

      Range
      5152..40929
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014649.3 → NP_055464.1  scaffold attachment factor B2

      See identical proteins and their annotated locations for NP_055464.1

      Status: REVIEWED

      Source sequence(s)
      AW136754, D50928, DB475007
      Consensus CDS
      CCDS32879.1
      UniProtKB/Swiss-Prot
      B4DKG3, Q14151, Q8TB13
      Related
      ENSP00000252542.3, ENST00000252542.9
      Conserved Domains (3) summary
      smart00513
      Location:30 → 64
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      COG0724
      Location:336 → 512
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12679
      Location:406 → 481
      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_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      5586999..5622776 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528449.4 → XP_011526751.1  scaffold attachment factor B2 isoform X1

      Conserved Domains (4) summary
      smart00513
      Location:30 → 64
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      COG0724
      Location:336 → 512
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12679
      Location:406 → 481
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins
      pfam08648
      Location:724 → 820
      DUF1777; Protein of unknown function (DUF1777)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      5573679..5609458 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322744.1 → XP_054178719.1  scaffold attachment factor B2 isoform X1

    2. XM_054322745.1 → XP_054178720.1  scaffold attachment factor B2 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14151.1 GenPept UniProtKB/Swiss-Prot:Q14151

    Gene LinkOut

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