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

Gene ID: 6294, updated on 10-Dec-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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. 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
  2. SAFB re-distribution marks steps of the apoptotic process. Lee YB, et al. Exp Cell Res, 2007 Nov 1. PMID 17643427
  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. High rates of loss of heterozygosity on chromosome 19p13 in human breast cancer. Oesterreich S, et al. Br J Cancer, 2001 Feb. PMID 11207044, Free PMC Article
  5. Short-term hypoxia triggers ROS and SAFB mediated nuclear matrix and mRNA splicing remodeling. Taze C, et al. Redox Biol, 2022 Dec. PMID 36427398, Free PMC Article

See all (189) 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)

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 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 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

    UniProtKB/TrEMBL
    B7Z1C7
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15424.4 GenPept UniProtKB/Swiss-Prot:Q15424

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