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

Gene ID: 9667, updated on 7-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (5586999..5622776, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (5573679..5609458, complement)
105.20220307 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
  • 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. 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
  2. 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
  3. SAFB1 mediates repression of immune regulators and apoptotic genes in breast cancer cells. Hammerich-Hille S, et al. J Biol Chem, 2010 Feb 5. PMID 19901029, Free PMC Article
  4. Low SAFB levels are associated with worse outcome in breast cancer patients. Hammerich-Hille S, et al. Breast Cancer Res Treat, 2010 Jun. PMID 19137425
  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 (104) 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_2023_10

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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