Human Gene SCRT2 (uc002wec.3)
  Description: Homo sapiens scratch homolog 2, zinc finger protein (Drosophila) (SCRT2), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr20:642,240-656,823 Size: 14,584 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr20:644,315-656,245 Size: 11,931 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:642,240-656,823)mRNA (may differ from genome)Protein (307 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SCRT2_HUMAN
DESCRIPTION: RecName: Full=Transcriptional repressor scratch 2; AltName: Full=Scratch homolog 2 zinc finger protein;
FUNCTION: May be involved in transcriptional regulation.
SUBCELLULAR LOCATION: Nucleus (Potential).
SIMILARITY: Belongs to the snail C2H2-type zinc-finger protein family.
SIMILARITY: Contains 5 C2H2-type zinc fingers.

-  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

+  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: 3.44 RPKM in Brain - Cerebellum
Total median expression: 10.57 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -198.79578-0.344 Picture PostScript Text
3' UTR -773.422075-0.373 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
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

Pfam Domains:
PF00096 - Zinc finger, C2H2 type
PF12874 - Zinc-finger of C2H2 type
PF13894 - C2H2-type zinc finger
PF13912 - C2H2-type zinc finger

SCOP Domains:
57667 - C2H2 and C2HC zinc fingers

ModBase Predicted Comparative 3D Structure on Q9NQ03
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 orthologGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
   FlyBase  
   Protein Sequence  
   Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
GO:2001222 regulation of neuron migration

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK125343 - Homo sapiens cDNA FLJ43353 fis, clone NT2RP7009867.
AY129025 - Homo sapiens clone FP7030 unknown mRNA.
BC172245 - Synthetic construct Homo sapiens clone IMAGE:100068939, MGC:198950 scratch homolog 2, zinc finger protein (Drosophila) (SCRT2) mRNA, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: FP7030, NM_033129, NP_149120, Q9NQ03, SCRT2_HUMAN
UCSC ID: uc002wec.3
RefSeq Accession: NM_033129
Protein: Q9NQ03 (aka SCRT2_HUMAN or SCR2_HUMAN)
CCDS: CCDS13006.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_033129.3
exon count: 2CDS single in 3' UTR: no RNA size: 3594
ORF size: 924CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1917.50frame shift in genome: no % Coverage: 99.53
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.