Human Gene SAFB (uc010xit.2)
  Description: Homo sapiens scaffold attachment factor B (SAFB), transcript variant 5, non-coding RNA.
Transcript (Including UTRs)
   Position: hg19 chr19:5,623,046-5,668,489 Size: 45,444 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg19 chr19:5,626,426-5,668,302 Size: 41,877 Coding Exon Count: 18 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:5,623,046-5,668,489)mRNA (may differ from genome)Protein (759 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsH-INV
HGNCLynxMGIPubMedUniProtKBWikipedia

-  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: 53.12 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 1683.14 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 -165.70370-0.448 Picture PostScript Text
3' UTR -34.40187-0.184 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

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

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on B7Z2F6
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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 Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0050684 regulation of mRNA processing


-  Descriptions from all associated GenBank mRNAs
  AK294718 - Homo sapiens cDNA FLJ56691 complete cds, highly similar to Scaffold attachment factor B.
AB208780 - Homo sapiens mRNA for scaffold attachment factor B variant protein.
AK307970 - Homo sapiens cDNA, FLJ97918.
AK295298 - Homo sapiens cDNA FLJ59523 complete cds, highly similar to Scaffold attachment factor B.
AK293152 - Homo sapiens cDNA FLJ59451 complete cds, highly similar to Scaffold attachment factor B.
AK095736 - Homo sapiens cDNA FLJ38417 fis, clone FEBRA2009731, highly similar to Human Hsp27 ERE-TATA-binding protein (HET) mRNA.
AK304474 - Homo sapiens cDNA FLJ54736 complete cds, highly similar to Scaffold attachment factor B.
AK298707 - Homo sapiens cDNA FLJ54745 complete cds, highly similar to Scaffold attachment factor B.
AK290444 - Homo sapiens cDNA FLJ76656 complete cds, highly similar to Homo sapiens scaffold attachment factor B (SAFB), mRNA.
BC020309 - Homo sapiens scaffold attachment factor B, mRNA (cDNA clone IMAGE:4999249).
BC032055 - Homo sapiens scaffold attachment factor B, mRNA (cDNA clone IMAGE:3919120).
U72355 - Human Hsp27 ERE-TATA-binding protein (HET) mRNA, complete cds.
BC126219 - Homo sapiens scaffold attachment factor B, mRNA (cDNA clone MGC:161497 IMAGE:8991935), complete cds.
BC143938 - Homo sapiens scaffold attachment factor B, mRNA (cDNA clone MGC:177473 IMAGE:9052456), complete cds.
BC143939 - Homo sapiens scaffold attachment factor B, mRNA (cDNA clone MGC:177474 IMAGE:9052457), complete cds.
BC143937 - Homo sapiens scaffold attachment factor B, mRNA (cDNA clone MGC:177472 IMAGE:9052455), complete cds.
AK299525 - Homo sapiens cDNA FLJ59404 complete cds, highly similar to Scaffold attachment factor B.
AK294671 - Homo sapiens cDNA FLJ54744 complete cds, highly similar to Scaffold attachment factor B.
L43631 - Homo sapiens scaffold attachment factor B (SAF-B) mRNA, partial cds.
JD312354 - Sequence 293378 from Patent EP1572962.
CR749251 - Homo sapiens mRNA; cDNA DKFZp779C1727 (from clone DKFZp779C1727).
JD299341 - Sequence 280365 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z2F6, B7Z2F6_HUMAN, NR_037699
UCSC ID: uc010xit.2
RefSeq Accession: NR_037699
Protein: B7Z2F6

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NR_037699.1
exon count: 19CDS single in 3' UTR: no RNA size: 2846
ORF size: 2280CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4561.00frame shift in genome: no % Coverage: 99.68
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.