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 factor... See more...

Aliases for SAFB Gene

Aliases for SAFB Gene

  • Scaffold Attachment Factor B 2 3 5
  • HSP27 Estrogen Response Element-TATA Box-Binding Protein 3 4
  • Hsp27 ERE-TATA Binding Protein 2 3
  • HSP27 ERE-TATA-Binding Protein 3 4
  • Scaffold Attachment Factor B1 3 4
  • SAF-B1 3 4
  • SAF-B 3 4
  • SAFB1 3 4
  • HAP 3 4
  • HET 3 4
  • Heat-Shock Protein (HSP27) Estrogen Response Element And TATA Box-Binding Protein 3
  • Glutathione S-Transferase Fusion Protein 3
  • SAB-B1 3

External Ids for SAFB Gene

Previous GeneCards Identifiers for SAFB Gene

  • GC19P005715
  • GC19P005563
  • GC19P005574
  • GC19P005384

Summaries for SAFB Gene

Entrez Gene Summary for SAFB Gene

  • 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]

GeneCards Summary for SAFB Gene

SAFB (Scaffold Attachment Factor B) is a Protein Coding gene. Diseases associated with SAFB include Denys-Drash Syndrome and Breast Cancer. Among its related pathways are Sertoli-Sertoli Cell Junction Dynamics and IL-1 signaling pathway. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is SAFB2.

UniProtKB/Swiss-Prot Summary for SAFB Gene

  • Binds to scaffold/matrix attachment region (S/MAR) DNA and forms a molecular assembly point to allow the formation of a 'transcriptosomal' complex (consisting of SR proteins and RNA polymerase II) coupling transcription and RNA processing (By similarity). Can function as an estrogen receptor corepressor and can also bind to the HSP27 promoter and decrease its transcription. When associated with RBMX, binds to and stimulates transcription from the SREBF1 promoter (By similarity). Can inhibit cell proliferation.

Gene Wiki entry for SAFB Gene

Additional gene information for SAFB Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SAFB Gene

Genomics for SAFB Gene

GeneHancer (GH) Regulatory Elements for SAFB Gene

Promoters and enhancers for SAFB Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SAFB on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SAFB

Top Transcription factor binding sites by QIAGEN in the SAFB gene promoter:
  • C/EBPbeta
  • CUTL1
  • FAC1
  • LyF-1
  • Pax-2
  • Pax-2a
  • Pax-5
  • Sp1
  • Zic3

Genomic Locations for SAFB Gene

Genomic Locations for SAFB Gene
chr19:5,623,035-5,668,478
(GRCh38/hg38)
Size:
45,444 bases
Orientation:
Plus strand
chr19:5,623,046-5,668,489
(GRCh37/hg19)
Size:
45,444 bases
Orientation:
Plus strand

Genomic View for SAFB Gene

Genes around SAFB on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SAFB Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SAFB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SAFB Gene

Proteins for SAFB Gene

  • Protein details for SAFB Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15424-SAFB1_HUMAN
    Recommended name:
    Scaffold attachment factor B1
    Protein Accession:
    Q15424
    Secondary Accessions:
    • A0AV56
    • B7Z5B6
    • B7ZLP6
    • F5H0H3
    • O60406
    • Q59HH8

    Protein attributes for SAFB Gene

    Size:
    915 amino acids
    Molecular mass:
    102642 Da
    Quaternary structure:
    • Monomer. Can form homodimers. Interacts with KHDRBS3, POLR2A, SAFB2 or SFRS1, SFRS9 and TRA2B/SFRS10 (By similarity). Interacts with isoform 1 and isoform 2 of SRPK1 and inhibits its activity. Interacts with RBMX (By similarity). Interacts with FUS.
    SequenceCaution:
    • Sequence=BAD92017.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SAFB Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SAFB Gene

Post-translational modifications for SAFB Gene

  • Sumoylated by PIAS1 with SUMO1 and SUMO2/3, desumoylated by SENP1. Sumoylation is required for transcriptional repressor activity.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SAFB Gene

Domains & Families for SAFB Gene

Gene Families for SAFB Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SAFB Gene

Blocks:
  • RNA-binding region RNP-1 (RNA recognition motif)
  • DNA-binding SAP
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SAFB Gene

GenScript: Design optimal peptide antigens:
  • Scaffold attachment factor B (A0AV56_HUMAN)
  • cDNA FLJ54744, highly similar to Scaffold attachment factor B (B7Z2F6_HUMAN)
  • cDNA FLJ54736, highly similar to Scaffold attachment factor B (B7Z959_HUMAN)
  • SAFB protein (B7ZLP5_HUMAN)
  • SAFB protein (B7ZLP6_HUMAN)
genes like me logo Genes that share domains with SAFB: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SAFB Gene

Function for SAFB Gene

Molecular function for SAFB Gene

UniProtKB/Swiss-Prot Function:
Binds to scaffold/matrix attachment region (S/MAR) DNA and forms a molecular assembly point to allow the formation of a 'transcriptosomal' complex (consisting of SR proteins and RNA polymerase II) coupling transcription and RNA processing (By similarity). Can function as an estrogen receptor corepressor and can also bind to the HSP27 promoter and decrease its transcription. When associated with RBMX, binds to and stimulates transcription from the SREBF1 promoter (By similarity). Can inhibit cell proliferation.
GENATLAS Biochemistry:
scaffold attachment factor B,97kDa,ubiquitously expressed protein (hsp27 promoter binding-protein)

Phenotypes From GWAS Catalog for SAFB Gene

Gene Ontology (GO) - Molecular Function for SAFB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding ISS --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA,ISS --
GO:0003690 double-stranded DNA binding TAS 1324173
genes like me logo Genes that share ontologies with SAFB: view
genes like me logo Genes that share phenotypes with SAFB: view

Animal Models for SAFB Gene

MGI Knock Outs for SAFB:

Animal Model Products

CRISPR Products

Clone Products

  • Addgene plasmids for SAFB

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SAFB Gene

Localization for SAFB Gene

Subcellular locations from UniProtKB/Swiss-Prot for SAFB Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SAFB gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SAFB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,TAS 21873635
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with SAFB: view

Pathways & Interactions for SAFB Gene

PathCards logo

SuperPathways for SAFB Gene

SuperPathway Contained pathways
1 Sertoli-Sertoli Cell Junction Dynamics
.36
2 IL-1 signaling pathway
genes like me logo Genes that share pathways with SAFB: view

Pathways by source for SAFB Gene

1 BioSystems pathway for SAFB Gene
1 Qiagen pathway for SAFB Gene
  • Epithelial Tight Junctions

Gene Ontology (GO) - Biological Process for SAFB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization TAS 1324173
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0030520 intracellular estrogen receptor signaling pathway IBA 21873635
GO:0040008 regulation of growth IEA --
genes like me logo Genes that share ontologies with SAFB: view

No data available for SIGNOR curated interactions for SAFB Gene

Drugs & Compounds for SAFB Gene

(16) Drugs for SAFB Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(15) Additional Compounds for SAFB Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SAFB: view

Transcripts for SAFB Gene

mRNA/cDNA for SAFB Gene

6 REFSEQ mRNAs :
22 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for SAFB

Alternative Splicing Database (ASD) splice patterns (SP) for SAFB Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15a · 15b ·
SP1: - - -
SP2:
SP3:
SP4:
SP5: - - - - - - -
SP6:
SP7: - - -
SP8:
SP9:
SP10:
SP11:

ExUns: 15c ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a · 20b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for SAFB Gene

GeneLoc Exon Structure for
SAFB

Expression for SAFB Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SAFB Gene

Protein differential expression in normal tissues from HIPED for SAFB Gene

This gene is overexpressed in Peripheral blood mononuclear cells (13.2), Nasal epithelium (6.8), and Testis (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SAFB Gene



Protein tissue co-expression partners for SAFB Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SAFB

SOURCE GeneReport for Unigene cluster for SAFB Gene:

Hs.728802

mRNA Expression by UniProt/SwissProt for SAFB Gene:

Q15424-SAFB1_HUMAN
Tissue specificity: Ubiquitous. Expressed at high levels in the CNS and at low levels in the liver. Expressed in a wide number of breast cancer cell lines.

Evidence on tissue expression from TISSUES for SAFB Gene

  • Nervous system(4.9)
  • Liver(4.3)
  • Lung(3.2)
  • Intestine(2.5)
genes like me logo Genes that share expression patterns with SAFB: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SAFB Gene

Orthologs for SAFB Gene

This gene was present in the common ancestor of animals.

Orthologs for SAFB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SAFB 31 30
  • 98.98 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SAFB 31 30
  • 89.62 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SAFB 31 30
  • 88.14 (n)
OneToMany
-- 31
  • 83 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Safb 17 31 30
  • 82.84 (n)
rat
(Rattus norvegicus)
Mammalia Safb 30
  • 81.81 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 74 (a)
ManyToMany
-- 31
  • 68 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 74 (a)
ManyToMany
-- 31
  • 69 (a)
ManyToMany
-- 31
  • 57 (a)
ManyToMany
-- 31
  • 53 (a)
ManyToMany
chicken
(Gallus gallus)
Aves SAFB2 30
  • 70.63 (n)
-- 31
  • 63 (a)
ManyToMany
-- 31
  • 62 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 49 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii safb 31 30
  • 56.07 (n)
OneToMany
Dr.2918 30
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10653 30
fruit fly
(Drosophila melanogaster)
Insecta Saf-B 31
  • 22 (a)
OneToMany
Species where no ortholog for SAFB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SAFB Gene

ENSEMBL:
Gene Tree for SAFB (if available)
TreeFam:
Gene Tree for SAFB (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SAFB: view image

Paralogs for SAFB Gene

Paralogs for SAFB Gene

(4) SIMAP similar genes for SAFB Gene using alignment to 6 proteins:

  • SAFB1_HUMAN
  • B7Z2F6_HUMAN
  • B7ZLP5_HUMAN
  • F5GZU3_HUMAN
  • K7EII0_HUMAN
  • K7ES42_HUMAN

Pseudogenes.org Pseudogenes for SAFB Gene

genes like me logo Genes that share paralogs with SAFB: view

Variants for SAFB Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SAFB Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
735932 Benign: not provided 5,649,932(+) C/T SYNONYMOUS_VARIANT
rs200429675 Uncertain Significance: not provided 5,667,105(+) G/C MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for SAFB Gene

Structural Variations from Database of Genomic Variants (DGV) for SAFB Gene

Variant ID Type Subtype PubMed ID
dgv652e214 CNV loss 21293372
esv2676285 CNV deletion 23128226
esv2718045 CNV deletion 23290073
esv275346 CNV gain+loss 21479260
esv3555929 CNV deletion 23714750
esv3643531 CNV loss 21293372
esv3643533 CNV gain 21293372
esv3643535 CNV loss 21293372
esv3643536 CNV loss 21293372
nsv1062851 CNV gain 25217958
nsv1072310 CNV deletion 25765185
nsv2395 CNV insertion 18451855
nsv953952 CNV deletion 24416366

Variation tolerance for SAFB Gene

Residual Variation Intolerance Score: 3.99% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.28; 25.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SAFB Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SAFB

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SAFB Gene

Disorders for SAFB Gene

MalaCards: The human disease database

(2) MalaCards diseases for SAFB Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
denys-drash syndrome
  • dds
breast cancer
  • breast cancer, familial
- elite association - COSMIC cancer census association via MalaCards
Search SAFB in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SAFB

genes like me logo Genes that share disorders with SAFB: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SAFB Gene

Publications for SAFB Gene

  1. Purification and molecular cloning of the scaffold attachment factor B (SAF-B), a novel human nuclear protein that specifically binds to S/MAR-DNA. (PMID: 8600450) Renz A … Fackelmayer FO (Nucleic acids research 1996) 2 3 4 23 54
  2. The enzymatic activity of SR protein kinases 1 and 1a is negatively affected by interaction with scaffold attachment factors B1 and 2. (PMID: 19674106) Tsianou D … Georgatsou E (The FEBS journal 2009) 3 4 23 54
  3. SAFB2, a new scaffold attachment factor homolog and estrogen receptor corepressor. (PMID: 12660241) Townson SM … Oesterreich S (The Journal of biological chemistry 2003) 3 4 23 54
  4. Cloning and characterization of an alternatively spliced form of SR protein kinase 1 that interacts specifically with scaffold attachment factor-B. (PMID: 11509566) Nikolakaki E … Giannakouros T (The Journal of biological chemistry 2001) 3 4 23 54
  5. SAF-B protein couples transcription and pre-mRNA splicing to SAR/MAR elements. (PMID: 9671816) Nayler O … Stamm S (Nucleic acids research 1998) 3 4 23 54

Products for SAFB Gene

Sources for SAFB Gene