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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
  • 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
  • Scaffold Attachment Factor B1 3
  • SAB-B1 3

External Ids for SAFB Gene

Previous GeneCards Identifiers for SAFB Gene

  • GC19P005715
  • GC19P005563
  • 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. Among its related pathways are Sertoli-Sertoli Cell Junction Dynamics. GO annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is SAFB2.

UniProtKB/Swiss-Prot 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SAFB Gene

Genomics for SAFB Gene

Regulatory Elements for SAFB Gene

Enhancers for SAFB Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19F005689 1.2 ENCODE 63.3 +69.1 69067 5.0 CREB3L1 ZFP64 DMAP1 YY1 ZNF143 ZNF548 ZNF263 SP3 SSRP1 ZNF610 SNRPEP4 ENSG00000267571 SAFB SAFB2 GTF2F1 VMAC RPL36 LONP1 LOC390877 ACSBG2
GH19F004866 1.5 FANTOM5 ENCODE 46.7 -754.4 -754382 5.7 HDGF PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 SNRPEP4 SAFB ENSG00000267030 DPP9-AS1 ENSG00000267769 SAFB2 ENSG00000269807 ENSG00000267255 PLIN3 SH3GL1
GH19F006527 1.2 ENCODE 51.4 +907.6 907609 6.2 HDGF PKNOX1 ARNT WRNIP1 ARID4B SIN3A YBX1 ZNF2 ZNF766 ZNF143 ZNF557 SNRPEP4 SAFB ENSG00000267571 SAFB2 GTF2F1 RPL36 LOC390877 FLJ25758 MBD3L5
GH19F006270 1.5 FANTOM5 ENCODE 41.1 +652.3 652318 10.7 HDGF PKNOX1 ARNT MLX CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF557 SNRPEP4 SAFB ENSG00000267571 VMAC ACSBG2 LOC390877 MBD3L3 MBD3L5 FLJ25758
GH19F005690 0.9 ENCODE 43.6 +66.4 66370 0.2 ZNF493 ZEB1 ZNF138 ZNF366 ZNF354C ZNF143 ZNF548 CREM ZNF202 ZNF362 SNRPEP4 ENSG00000267571 SAFB SAFB2 GTF2F1 RPL36 C19orf70 GC19P005701
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SAFB on UCSC Golden Path with GeneCards custom track

Promoters for SAFB Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000140024 165 3201 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9

Genomic Location for SAFB Gene

Chromosome:
19
Start:
5,623,035 bp from pter
End:
5,668,478 bp from pter
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).
    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

Antibody Products

  • Abcam antibodies for SAFB

No data available for DME Specific Peptides for SAFB Gene

Domains & Families for SAFB Gene

Gene Families for SAFB Gene

Graphical View of Domain Structure for InterPro Entry

Q15424

UniProtKB/Swiss-Prot:

SAFB1_HUMAN :
  • Contains 1 RRM (RNA recognition motif) domain.
Domain:
  • Contains 1 RRM (RNA recognition motif) domain.
  • Contains 1 SAP domain.
genes like me logo Genes that share domains with SAFB: view

Function for SAFB Gene

Molecular function for SAFB Gene

GENATLAS Biochemistry:
scaffold attachment factor B,97kDa,ubiquitously expressed protein (hsp27 promoter binding-protein)
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.

Gene Ontology (GO) - Molecular Function for SAFB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0001047 core promoter binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
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

Flow Cytometry Products

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

Gene Ontology (GO) - Cellular Components for SAFB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 1324173
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with SAFB: view

Pathways & Interactions for SAFB Gene

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

Pathways by source for SAFB Gene

1 Qiagen pathway for SAFB Gene

Gene Ontology (GO) - Biological Process for SAFB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization TAS 1324173
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription from RNA polymerase II promoter IBA --
GO:0030520 intracellular estrogen receptor signaling pathway IEA,IBA --
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

(17) Drugs for SAFB Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(14) 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

Unigene Clusters for SAFB Gene

Scaffold attachment factor B:
Representative Sequences:

Flow Cytometry Products

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
ECgene alternative splicing isoforms 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, PaxDb, MaxQB, and MOPED for SAFB Gene



Protein tissue co-expression partners for SAFB Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SAFB Gene:

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.
genes like me logo Genes that share expression patterns with SAFB: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues 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 34 35
  • 98.98 (n)
dog
(Canis familiaris)
Mammalia SAFB 34 35
  • 89.62 (n)
cow
(Bos Taurus)
Mammalia SAFB 34 35
  • 88.14 (n)
-- 35
  • 83 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Safb 34 16 35
  • 82.84 (n)
rat
(Rattus norvegicus)
Mammalia Safb 34
  • 81.81 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 74 (a)
ManyToMany
-- 35
  • 68 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 74 (a)
ManyToMany
-- 35
  • 69 (a)
ManyToMany
-- 35
  • 57 (a)
ManyToMany
-- 35
  • 53 (a)
ManyToMany
chicken
(Gallus gallus)
Aves SAFB2 34
  • 70.63 (n)
-- 35
  • 63 (a)
ManyToMany
-- 35
  • 62 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 49 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii safb 34 35
  • 56.07 (n)
Dr.2918 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10653 34
fruit fly
(Drosophila melanogaster)
Insecta Saf-B 35
  • 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)

Paralogs for SAFB Gene

Paralogs for SAFB Gene

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

Pseudogenes.org Pseudogenes for SAFB Gene

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

Variants for SAFB Gene

Sequence variations from dbSNP and Humsavar for SAFB Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs10401899 -- 5,650,340(+) AACAG(C/T)GCATT intron-variant
rs10402316 -- 5,628,205(+) cagat(C/T)gcacc intron-variant
rs10402699 -- 5,637,519(+) agcat(C/G)gtggc intron-variant
rs10405580 -- 5,633,992(+) TGCTA(C/G)CTGGT intron-variant
rs10407593 -- 5,668,586(+) TTATT(A/T)TTTTT downstream-variant-500B

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

Variant ID Type Subtype PubMed ID
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
esv3643531 CNV loss 21293372
esv3555929 CNV deletion 23714750
esv275346 CNV gain+loss 21479260
esv2718045 CNV deletion 23290073
esv2676285 CNV deletion 23128226
dgv652e214 CNV loss 21293372

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)

Relevant External Links for SAFB Gene

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

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

Disorders for SAFB Gene

Relevant External Links for SAFB

Human Genome Epidemiology (HuGE) Navigator
SAFB
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SAFB

No disorders were found for SAFB Gene.

No data available for MalaCards , 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 F.O. (Nucleic Acids Res. 1996) 2 3 4 22 64
  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. (FEBS J. 2009) 3 4 22 64
  3. SAFB2, a new scaffold attachment factor homolog and estrogen receptor corepressor. (PMID: 12660241) Townson S.M. … Oesterreich S. (J. Biol. Chem. 2003) 3 4 22 64
  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. (J. Biol. Chem. 2001) 3 4 22 64
  5. SAF-B couples transcription and pre-mRNA splicing to SAR/MAR elements. (PMID: 9671816) Nayler O. … Stamm S. (Nucleic Acids Res. 1998) 3 4 22 64

Products for SAFB Gene

Sources for SAFB Gene

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