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

Gene ID: 6294, updated on 1-Jun-2020

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
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

Genomic context

See SAFB in Genome Data Viewer
Location:
19p13.3
Exon count:
21
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (5623081..5668478)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (5623046..5668489)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory regions 733 and 12449 Neighboring gene scaffold attachment factor B2 Neighboring gene uncharacterized LOC107985320 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

Homology

Clone Names

  • DKFZp779C1727

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
double-stranded DNA binding TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
chromatin organization TAS
Traceable Author Statement
more info
PubMed 
hormone metabolic process IEA
Inferred from Electronic Annotation
more info
 
intracellular estrogen receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
regulation of growth IEA
Inferred from Electronic Annotation
more info
 
regulation of mRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
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)

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/Swiss-Prot
    Q15424
    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/Swiss-Prot
    Q15424
    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/Swiss-Prot
    Q15424
    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/Swiss-Prot
    Q15424
    UniProtKB/TrEMBL
    B7Z2F6
    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/Swiss-Prot
    Q15424
    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
    Q15424
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    5623081..5668478
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

  2. XM_017027115.1XP_016882604.1  scaffold attachment factor B1 isoform X2

  3. XM_017027116.1XP_016882605.1  scaffold attachment factor B1 isoform X3

  4. XM_017027117.1XP_016882606.1  scaffold attachment factor B1 isoform X4

  5. XM_017027118.1XP_016882607.1  scaffold attachment factor B1 isoform X5

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