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Aliases for SAFB Gene

Aliases for SAFB Gene

  • Scaffold Attachment Factor B 2 3
  • HET 3 4 6
  • 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
  • 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. Diseases associated with SAFB include cysticercosis and denys-drash syndrome. Among its related pathways are Sertoli-Sertoli Cell Junction Dynamics. GO annotations related to this gene include RNA binding and nucleotide binding. An important paralog of this gene is SLTM.

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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for SAFB Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for SAFB Gene at MOPED

Post-translational modifications for SAFB Gene

  • Sumoylated by PIAS1 with SUMO1 and SUMO2/3, desumoylated by SENP1. Sumoylation is required for transcriptional repressor activity.
  • Ubiquitination at Lys294, Lys423, and Lys428
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SAFB Gene

Domains for SAFB Gene

Gene Families for SAFB Gene

HGNC:
  • RBM :RNA binding motif (RRM) containing

Graphical View of Domain Structure for InterPro Entry

Q15424

UniProtKB/Swiss-Prot:

SAFB1_HUMAN :
  • Q15424
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 --
GO:0003682 chromatin binding IEA --
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

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for SAFB Gene

Localization for SAFB Gene

Subcellular locations from UniProtKB/Swiss-Prot for SAFB Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SAFB Gene 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 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

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

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:0030520 intracellular estrogen receptor signaling pathway IEA --
GO:0040007 growth IEA --
GO:0042445 hormone metabolic process IEA --
genes like me logo Genes that share ontologies with SAFB: view

Compounds for SAFB Gene

(31) Novoseek inferred chemical compound relationships for SAFB Gene

Compound -log(P) Hits PubMed IDs
tyrosine 58.1 18
phosphotyrosine 50.9 3
gdp 48.3 3
phosphatidylinositol 45.8 5
serine 41.7 4
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:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SAFB

Primer Products

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 for SAFB Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues 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 from ProteomicsDB, PaxDb, MOPED, and MaxQB for SAFB Gene

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 expressions with SAFB: view

Expression partners for SAFB Gene

In Situ Assay Products

No data available for 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
cow
(Bos Taurus)
Mammalia SAFB 35
  • 88.14 (n)
  • 90.35 (a)
-- 36
  • 83 (a)
OneToMany
SAFB 36
  • 88 (a)
OneToMany
dog
(Canis familiaris)
Mammalia SAFB 35
  • 89.62 (n)
  • 92.31 (a)
SAFB 36
  • 80 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Safb 35
  • 82.84 (n)
  • 86.64 (a)
Safb 16
Safb 36
  • 83 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SAFB 35
  • 98.98 (n)
  • 98.91 (a)
SAFB 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Safb 35
  • 81.81 (n)
  • 85.3 (a)
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 68 (a)
ManyToMany
-- 36
  • 74 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 53 (a)
ManyToMany
-- 36
  • 57 (a)
ManyToMany
-- 36
  • 69 (a)
ManyToMany
-- 36
  • 74 (a)
ManyToMany
chicken
(Gallus gallus)
Aves SAFB2 35
  • 70.63 (n)
  • 67.42 (a)
-- 36
  • 63 (a)
ManyToMany
-- 36
  • 62 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 49 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii Dr.2918 35
safb 35
  • 56.07 (n)
  • 51.62 (a)
safb 36
  • 43 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10653 35
fruit fly
(Drosophila melanogaster)
Insecta Saf-B 36
  • 22 (a)
OneToMany
Species with no ortholog for SAFB:
  • 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

Selected 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 MAF
rs14765 -- 5,667,085(+) ACGGC(A/C)GGGAC synonymous-codon, reference, nc-transcript-variant
rs1046382 -- 5,664,100(-) AAGCG(C/G)TCCTG reference, missense, nc-transcript-variant
rs1129046 -- 5,654,438(-) CCGGA(C/T)GTTTT synonymous-codon, reference, nc-transcript-variant
rs1538011 -- 5,664,025(+) AGGCG(A/T)GATGA reference, synonymous-codon, nc-transcript-variant
rs1538012 -- 5,664,601(+) TTTGG(A/G)ATTAT intron-variant

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

Variant ID Type Subtype PubMed ID
dgv3693n71 CNV Loss 21882294
nsv2395 CNV Insertion 18451855
esv2676285 CNV Deletion 23128226
esv2718045 CNV Deletion 23290073
esv275346 CNV Gain+Loss 21479260
nsv910894 CNV Loss 21882294
dgv3694n71 CNV Loss 21882294

Relevant External Links for SAFB Gene

HapMap Linkage Disequilibrium report
SAFB

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

Disorders for SAFB Gene

MalaCards: The human disease database

MalaCards: The human disease database.

Search for SAFB Gene in MalaCards »

(3) Diseases for SAFB Gene including...

(10) Novoseek inferred disease relationships for SAFB Gene

Disease -log(P) Hits PubMed IDs
hydatids 19.6 1
cysticercosis 8.49 1
breast cancer 4.31 7
leukemia 4.3 1
cancer 2.43 1

Relevant External Links for SAFB

Human Genome Epidemiology (HuGE) Navigator
SAFB
genes like me logo Genes that share disorders with SAFB: view

No data available for OMIM , UniProtKB/Swiss-Prot , University of Copenhagen DISEASES 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 23
  2. Assignment of SAFB encoding Hsp27 ERE-TATA binding protein (HET)/scaffold attachment factor B (SAF-B) to human chromosome 19 band p13. (PMID: 9605873) DuPont B.R. … Oesterreich S. (Cytogenet. Cell Genet. 1997) 2 3 23
  3. SAF-B couples transcription and pre-mRNA splicing to SAR/MAR elements. (PMID: 9671816) Nayler O. … Stamm S. (Nucleic Acids Res. 1998) 3 4 23
  4. Novel nuclear matrix protein HET binds to and influences activity of the HSP27 promoter in human breast cancer cells. (PMID: 9328833) Oesterreich S. … Fuqua S.A.W. (J. Cell. Biochem. 1997) 3 4 23
  5. 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 23

Products for SAFB Gene

  • Addgene plasmids for SAFB

Sources for SAFB Gene

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