Human Gene SAFB2 (ENST00000252542.9_8) from GENCODE V47lift37
  Description: scaffold attachment factor B2 (from RefSeq NM_014649.3)
Gencode Transcript: ENST00000252542.9_8
Gencode Gene: ENSG00000130254.13_13
Transcript (Including UTRs)
   Position: hg19 chr19:5,587,010-5,622,787 Size: 35,778 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr19:5,587,254-5,622,726 Size: 35,473 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:5,587,010-5,622,787)mRNA (may differ from genome)Protein (953 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SAFB2_HUMAN
DESCRIPTION: RecName: Full=Scaffold attachment factor B2; Short=SAF-B2;
FUNCTION: Binds to scaffold/matrix attachment region (S/MAR) DNA. Can function as an estrogen receptor corepressor and can also inhibit cell proliferation.
SUBUNIT: Interacts with SAFB/SAFB1 and SCAM1. Interacts with isoform 2 SRPK1 and inhibits its activity.
INTERACTION: P03372:ESR1; NbExp=2; IntAct=EBI-352869, EBI-78473; Q9H0R8:GABARAPL1; NbExp=2; IntAct=EBI-352869, EBI-3464833; Q9GZQ8:MAP1LC3B; NbExp=3; IntAct=EBI-352869, EBI-373144; Q15424:SAFB; NbExp=3; IntAct=EBI-352869, EBI-348298; O60504-2:SORBS3; NbExp=3; IntAct=EBI-352869, EBI-1222956;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Expressed at high levels in the CNS and at low levels in the liver. Expressed in a wide number of breast cancer cell lines.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR (By similarity).
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SIMILARITY: Contains 1 SAP domain.
SEQUENCE CAUTION: Sequence=BAA09487.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 39.53 RPKM in Brain - Cerebellum
Total median expression: 1006.05 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -20.8061-0.341 Picture PostScript Text
3' UTR -50.70244-0.208 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom
IPR003034 - SAP_DNA-bd

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF02037 - SAP domain
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
68906 - SAP domain
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q14151
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003690 double-stranded DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0042802 identical protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0050684 regulation of mRNA processing
GO:0060008 Sertoli cell differentiation
GO:0060765 regulation of androgen receptor signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0016604 nuclear body
GO:0043231 intracellular membrane-bounded organelle
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  D50928 - Homo sapiens mRNA for KIAA0138 gene.
JD508234 - Sequence 489258 from Patent EP1572962.
JD527228 - Sequence 508252 from Patent EP1572962.
AB463241 - Synthetic construct DNA, clone: pF1KA0138, Homo sapiens SAFB2 gene for scaffold attachment factor B2, without stop codon, in Flexi system.
AK123246 - Homo sapiens cDNA FLJ41252 fis, clone BRAMY2033316.
KJ902004 - Synthetic construct Homo sapiens clone ccsbBroadEn_11398 SAFB2 gene, encodes complete protein.
BC025279 - Homo sapiens scaffold attachment factor B2, mRNA (cDNA clone MGC:39189 IMAGE:5258272), complete cds.
BC014784 - Homo sapiens scaffold attachment factor B2, mRNA (cDNA clone IMAGE:4215161), partial cds.
BC001216 - Homo sapiens scaffold attachment factor B2, mRNA (cDNA clone IMAGE:3534777), partial cds.
AK296552 - Homo sapiens cDNA FLJ60631 complete cds, moderately similar to Scaffold attachment factor B2.
AK300501 - Homo sapiens cDNA FLJ57435 complete cds, highly similar to Scaffold attachment factor B2.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DKG3, ENST00000252542.1, ENST00000252542.2, ENST00000252542.3, ENST00000252542.4, ENST00000252542.5, ENST00000252542.6, ENST00000252542.7, ENST00000252542.8, KIAA0138, NM_014649, Q14151, Q8TB13, SAFB2_HUMAN, uc317fhr.1, uc317fhr.2
UCSC ID: ENST00000252542.9_8
RefSeq Accession: NM_014649.3
Protein: Q14151 (aka SAFB2_HUMAN or SFB2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.