Human Gene ZNF280C (uc004evm.3)
  Description: Homo sapiens zinc finger protein 280C (ZNF280C), mRNA.
RefSeq Summary (NM_017666): This gene encodes a member of the zinc finger domain-containing protein family. This family member contains multiple Cys2-His2(C2H2)-type zinc finger domains, the most common type of zinc finger domain that self-folds to form a beta-beta-alpha structure that binds a zinc ion. [provided by RefSeq, Aug 2011]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Transcript (Including UTRs)
   Position: hg19 chrX:129,336,673-129,402,922 Size: 66,250 Total Exon Count: 19 Strand: -
Coding Region
   Position: hg19 chrX:129,338,951-129,394,423 Size: 55,473 Coding Exon Count: 18 

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 (chrX:129,336,673-129,402,922)mRNA (may differ from genome)Protein (737 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: Z280C_HUMAN
DESCRIPTION: RecName: Full=Zinc finger protein 280C; AltName: Full=Suppressor of hairy wing homolog 3; AltName: Full=Zinc finger protein 633;
FUNCTION: May function as a transcription factor.
SUBCELLULAR LOCATION: Nucleus (Potential).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 5 C2H2-type zinc fingers.
SEQUENCE CAUTION: Sequence=BAA90947.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;

-  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: 5.16 RPKM in Testis
Total median expression: 61.88 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 -65.30203-0.322 Picture PostScript Text
3' UTR -549.022278-0.241 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
IPR025243 - DUF4195
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like

Pfam Domains:
PF13836 - Domain of unknown function (DUF4195)

SCOP Domains:
57667 - C2H2 and C2HC zinc fingers

ModBase Predicted Comparative 3D Structure on Q8ND82
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 Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0046872 metal ion 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

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC051728 - Homo sapiens zinc finger protein 280C, mRNA (cDNA clone MGC:48650 IMAGE:4828435), complete cds.
AL834333 - Homo sapiens mRNA; cDNA DKFZp434P2272 (from clone DKFZp434P2272).
AK290373 - Homo sapiens cDNA FLJ76089 complete cds, highly similar to Homo sapiens suppressor of hairy wing homolog 3 (Drosophila) (SUHW3), mRNA.
KJ899156 - Synthetic construct Homo sapiens clone ccsbBroadEn_08550 ZNF280C gene, encodes complete protein.
AL133204 - Novel human gene mapping to chomosome X.
AK000102 - Homo sapiens cDNA FLJ20095 fis, clone COL04372.
JD080207 - Sequence 61231 from Patent EP1572962.
JD492822 - Sequence 473846 from Patent EP1572962.
JD079322 - Sequence 60346 from Patent EP1572962.
JD551367 - Sequence 532391 from Patent EP1572962.
JD088139 - Sequence 69163 from Patent EP1572962.
JD561268 - Sequence 542292 from Patent EP1572962.
JD354673 - Sequence 335697 from Patent EP1572962.
JD385549 - Sequence 366573 from Patent EP1572962.
JD026981 - Sequence 8005 from Patent EP1572962.
JD483969 - Sequence 464993 from Patent EP1572962.
JD377237 - Sequence 358261 from Patent EP1572962.
JD101277 - Sequence 82301 from Patent EP1572962.
JD254503 - Sequence 235527 from Patent EP1572962.
JD254110 - Sequence 235134 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K2V8, NM_017666, NP_060136, Q8ND82, Q9NXR3, SUHW3, Z280C_HUMAN, ZNF633
UCSC ID: uc004evm.3
RefSeq Accession: NM_017666
Protein: Q8ND82 (aka Z280C_HUMAN)
CCDS: CCDS14622.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_017666.4
exon count: 19CDS single in 3' UTR: no RNA size: 4695
ORF size: 2214CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4560.00frame shift in genome: no % Coverage: 100.00
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.