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    SAFB scaffold attachment factor B [ Homo sapiens (human) ]

    Gene ID: 6294, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SAFBprovided by HGNC
    Official Full Name
    scaffold attachment factor Bprovided by HGNC
    Primary source
    HGNC:HGNC:10520
    See related
    Ensembl:ENSG00000160633 MIM:602895; AllianceGenome:HGNC:10520
    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
    Also known as
    HAP; HET; SAF-B; SAFB1; SAB-B1; SAF-B1
    Summary
    This gene encodes a DNA-binding protein which has high specificity for scaffold or matrix attachment region DNA elements (S/MAR DNA). This protein is thought to be involved in attaching the base of chromatin loops to the nuclear matrix but there is conflicting evidence as to whether this protein is a component of chromatin or a nuclear matrix protein. Scaffold attachment factors are a specific subset of nuclear matrix proteins (NMP) that specifically bind to S/MAR. The encoded protein is thought to serve as a molecular base to assemble a 'transcriptosome complex' in the vicinity of actively transcribed genes. It is involved in the regulation of heat shock protein 27 transcription, can act as an estrogen receptor co-repressor and is a candidate for breast tumorigenesis. This gene is arranged head-to-head with a similar gene whose product has the same functions. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]
    Expression
    Ubiquitous expression in spleen (RPKM 29.9), testis (RPKM 26.5) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See SAFB 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 (5623083..5668478)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (5609766..5655162)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (5623094..5668489)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes 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 scaffold attachment factor B2 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 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 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13809 Neighboring gene mitochondrial contact site and cristae organizing system subunit 13

    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. Characterization of SAF-A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elements. Romig H, et al. EMBO J, 1992 Sep. PMID 1324173, Free PMC Article
    2. Downregulation of SAFB Sustains the NF-κB Pathway by Targeting TAK1 during the Progression of Colorectal Cancer. Jiao HL, et al. Clin Cancer Res, 2017 Nov 15. PMID 28912140
    3. Scaffold attachment factor B suppresses HIV-1 infection of CD4(+) T cells by preventing binding of RNA polymerase II to HIV-1's long terminal repeat. Ma L, et al. J Biol Chem, 2018 Aug 3. PMID 29887524, Free PMC Article
    4. The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation. Huo X, et al. Mol Cell, 2020 Jan 16. PMID 31677973
    5. Abnormal scaffold attachment factor 1 expression and localization in spinocerebellar ataxias and Huntington's chorea. Buckner N, et al. Brain Pathol, 2020 Nov. PMID 32580238, Free PMC Article

    See all (188) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia.
      Title: HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia.
    2. SKA1 promotes tumor metastasis via SAFB-mediated transcription repression of DUSP6 in clear cell renal cell carcinoma.
      Title: SKA1 promotes tumor metastasis via SAFB-mediated transcription repression of DUSP6 in clear cell renal cell carcinoma.
    3. Short-term hypoxia triggers ROS and SAFB mediated nuclear matrix and mRNA splicing remodeling.
      Title: Short-term hypoxia triggers ROS and SAFB mediated nuclear matrix and mRNA splicing remodeling.
    4. Subcellular dynamics of estrogen-related receptors involved in transrepression through interactions with scaffold attachment factor B1.
      Title: Subcellular dynamics of estrogen-related receptors involved in transrepression through interactions with scaffold attachment factor B1.
    5. Abnormal scaffold attachment factor 1 expression and localization in spinocerebellar ataxias and Huntington's chorea.
      Title: Abnormal scaffold attachment factor 1 expression and localization in spinocerebellar ataxias and Huntington's chorea.
    6. Inhibition of HSF1 and SAFB Granule Formation Enhances Apoptosis Induced by Heat Stress.
      Title: Inhibition of HSF1 and SAFB Granule Formation Enhances Apoptosis Induced by Heat Stress.
    7. Scaffold association factor B (SAFB) is required for expression of prenyltransferases and RAS membrane association.
      Title: Scaffold association factor B (SAFB) is required for expression of prenyltransferases and RAS membrane association.
    8. Depletion of SAFB leads to changes in 3D genome organization.
      Title: The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation.
    9. SAFB1 binds to the HIV-1 LTR and physically interacts with phosphorylated RNA polymerase II, repressing HIV-1 transcription initiation and elongation.
      Title: Scaffold attachment factor B suppresses HIV-1 infection of CD4(+) T cells by preventing binding of RNA polymerase II to HIV-1's long terminal repeat.
    10. SAFB regulated the activity of NF-kappaB signaling in CRC by targeting TAK1 This novel mechanism provides a comprehensive understanding of both SAFB and the NF-kappaB signaling pathway in the progression of CRC and indicates that the SAFB-TAK1-NF-kappaB axis is a potential target for early therapeutic intervention in CRC progression
      Title: Downregulation of SAFB Sustains the NF-κB Pathway by Targeting TAK1 during the Progression of Colorectal Cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (35)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify scaffold attachment factor B (SAFB), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify scaffold attachment factor B (SAFB), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify scaffold attachment factor B (SAFB), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify scaffold attachment factor B (SAFB), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Rev rev HIV-1 Rev interacting protein, scaffold attachment factor B (SAFB), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with SAFB is increased by RRE PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Clone Names

    • DKFZp779C1727

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables double-stranded DNA binding TAS
    Traceable Author Statement
    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 chromatin organization TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in estrogen 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 midbody IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    scaffold attachment factor B1
    Names
    HSP27 ERE-TATA-binding protein
    HSP27 estrogen response element-TATA box-binding protein
    Hsp27 ERE-TATA binding protein
    glutathione S-transferase fusion protein
    heat-shock protein (HSP27) estrogen response element and TATA box-binding protein

    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_001201338.2 → NP_001188267.1  scaffold attachment factor B1 isoform 1

      See identical proteins and their annotated locations for NP_001188267.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1).
      Source sequence(s)
      AC004611, AC011499, BC126219, CN271637
      Consensus CDS
      CCDS59339.1
      UniProtKB/TrEMBL
      A8K329
      Related
      ENSP00000467423.1, ENST00000588852.2
      Conserved Domains (2) summary
      smart00513
      Location:31 → 65
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd12679
      Location:405 → 480
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

    2. NM_001201339.2 → NP_001188268.1  scaffold attachment factor B1 isoform 2

      See identical proteins and their annotated locations for NP_001188268.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
      Source sequence(s)
      AC004611, BC143939, CN271637
      Consensus CDS
      CCDS59340.1
      UniProtKB/TrEMBL
      A8K329
      Related
      ENSP00000464840.1, ENST00000592224.5
      Conserved Domains (2) summary
      smart00513
      Location:31 → 65
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd12679
      Location:405 → 480
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

    3. NM_001201340.2 → NP_001188269.1  scaffold attachment factor B1 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting protein (isoform 4) is shorter compared to isoform 1.
      Source sequence(s)
      AC004611, AC011499, AC134303, AK298707, CN271637
      Consensus CDS
      CCDS56077.1
      UniProtKB/TrEMBL
      B7Z2Z1
      Related
      ENSP00000415895.1, ENST00000454510.5
      Conserved Domains (2) summary
      smart00513
      Location:31 → 65
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd12679
      Location:336 → 411
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

    4. NM_001320571.2 → NP_001307500.1  scaffold attachment factor B1 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two exons in the 5' coding region and uses an alternate start codon, which results in a frameshift compared to variant 1. The encoded isoform (5) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AK294671, DC349269, U72355
      UniProtKB/TrEMBL
      B7Z2F6, B7Z5X3
      Conserved Domains (1) summary
      cd12679
      Location:248 → 323
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

    5. NM_001320572.2 → NP_001307501.1  scaffold attachment factor B1 isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (6) is shorter than isoform 1.
      Source sequence(s)
      BC143938, DC349269, U72355
      UniProtKB/TrEMBL
      B7ZLP5
      Conserved Domains (2) summary
      smart00513
      Location:31 → 65
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd12679
      Location:405 → 480
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

    6. NM_002967.4 → NP_002958.2  scaffold attachment factor B1 isoform 3

      See identical proteins and their annotated locations for NP_002958.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The resulting protein (isoform 3) is shorter compared to isoform 1.
      Source sequence(s)
      AC004611, BC020309, CN271637, L43631
      Consensus CDS
      CCDS12142.1
      UniProtKB/Swiss-Prot
      A0AV56, B7Z5B6, B7ZLP6, F5H0H3, O60406, Q15424, Q59HH8
      UniProtKB/TrEMBL
      B7ZLP5
      Related
      ENSP00000292123.4, ENST00000292123.9
      Conserved Domains (2) summary
      smart00513
      Location:31 → 65
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd12679
      Location:405 → 480
      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
      5623083..5668478
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017027114.2 → XP_016882603.1  scaffold attachment factor B1 isoform X1

      UniProtKB/TrEMBL
      B7Z1C7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      5609766..5655162
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321710.1 → XP_054177685.1  scaffold attachment factor B1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15424.4 GenPept UniProtKB/Swiss-Prot:Q15424

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