Human Gene ZNF256 (uc002qqu.3)
  Description: Homo sapiens zinc finger protein 256 (ZNF256), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr19:58,452,201-58,459,077 Size: 6,877 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr19:58,452,292-58,458,842 Size: 6,551 Coding Exon Count: 3 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:58,452,201-58,459,077)mRNA (may differ from genome)Protein (627 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ZN256_HUMAN
DESCRIPTION: RecName: Full=Zinc finger protein 256; AltName: Full=Bone marrow zinc finger 3; Short=BMZF-3;
FUNCTION: Transcriptional repressor that plays a role in cell proliferation. Requires TRIM28 for its activity.
SUBUNIT: Interacts with TRIM28.
SUBCELLULAR LOCATION: Nucleus.
INDUCTION: By GDNF/glial cell line-derived neurotrophic factor.
DOMAIN: The KRAB domain mediates interaction with TRIM28 and is required for transcriptional repressor activity.
SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein family.
SIMILARITY: Contains 15 C2H2-type zinc fingers.
SIMILARITY: Contains 1 KRAB domain.

-  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: 4.63 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 115.16 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 -95.90235-0.408 Picture PostScript Text
3' UTR -11.9091-0.131 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
IPR001909 - Krueppel-associated_box
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

Pfam Domains:
PF00096 - Zinc finger, C2H2 type
PF01352 - KRAB box
PF13894 - C2H2-type zinc finger
PF13912 - C2H2-type zinc finger

SCOP Domains:
48695 - Multiheme cytochromes
109640 - KRAB domain (Kruppel-associated box, Pfam 01352)
57667 - C2H2 and C2HC zinc fingers

ModBase Predicted Comparative 3D Structure on Q9Y2P7
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 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:0003700 transcription factor activity, sequence-specific 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
GO:0007275 multicellular organism development
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC001438 - Homo sapiens zinc finger protein 256, mRNA (cDNA clone MGC:1413 IMAGE:3138611), complete cds.
AK314094 - Homo sapiens cDNA, FLJ94777, highly similar to Homo sapiens zinc finger protein 256 (ZNF256), mRNA.
AB464386 - Synthetic construct DNA, clone: pF1KB7856, Homo sapiens ZNF256 gene for zinc finger protein 256, without stop codon, in Flexi system.
AF067165 - Homo sapiens zinc finger protein 3 mRNA, complete cds.
BT006853 - Homo sapiens zinc finger protein 256 mRNA, complete cds.
KJ902070 - Synthetic construct Homo sapiens clone ccsbBroadEn_11464 ZNF256 gene, encodes complete protein.
CU674704 - Synthetic construct Homo sapiens gateway clone IMAGE:100018331 5' read ZNF256 mRNA.
DQ594220 - Homo sapiens piRNA piR-60332, complete sequence.
JD181376 - Sequence 162400 from Patent EP1572962.
JD316378 - Sequence 297402 from Patent EP1572962.
JD102266 - Sequence 83290 from Patent EP1572962.
JD316515 - Sequence 297539 from Patent EP1572962.
JD386823 - Sequence 367847 from Patent EP1572962.
JD044929 - Sequence 25953 from Patent EP1572962.
JD084550 - Sequence 65574 from Patent EP1572962.
JD207090 - Sequence 188114 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y2P7 (Reactome details) participates in the following event(s):

R-HSA-975040 KRAB-ZNF / KAP Interaction
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B2RA92, BMZF3, NM_005773, NP_005764, Q53Y85, Q9BV71, Q9Y2P7, ZN256_HUMAN
UCSC ID: uc002qqu.3
RefSeq Accession: NM_005773
Protein: Q9Y2P7 (aka ZN256_HUMAN or Z256_HUMAN)
CCDS: CCDS12966.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005773.2
exon count: 3CDS single in 3' UTR: no RNA size: 2228
ORF size: 1884CDS single in intron: no Alignment % ID: 99.95
txCdsPredict score: 3968.00frame shift in genome: no % Coverage: 99.19
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.