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

    Gene ID: 6294, updated on 19-Jun-2024

    Summary

    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
    NEW
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    Genomic context

    See SAFB 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 (5623083..5668478)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (5609766..5655162)
    105.20220307 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_001201338.2NP_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:3165
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd12679
      Location:405480
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins
    2. NM_001201339.2NP_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:3165
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd12679
      Location:405480
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins
    3. NM_001201340.2NP_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:3165
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd12679
      Location:336411
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins
    4. NM_001320571.2NP_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:248323
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins
    5. NM_001320572.2NP_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:3165
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd12679
      Location:405480
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins
    6. NM_002967.4NP_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:3165
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd12679
      Location:405480
      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
      5623083..5668478
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017027114.2XP_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_054321710.1XP_054177685.1  scaffold attachment factor B1 isoform X1

      UniProtKB/TrEMBL
      B7Z1C7