Human Gene ZNF304 (uc010ygw.2)
  Description: Homo sapiens zinc finger protein 304 (ZNF304), mRNA.
RefSeq Summary (NM_020657): This gene encodes a member of the Krueppel C2H2-type zinc-finger family of proteins. The encoded protein functions as a transcriptional repressor that recruits a corepressor complex to stimulate promoter hypermethylation and transcriptional silencing of target genes. Expression of this gene is upregulated in colorectal, ovarian and breast cancer, and this gene may promote cancer cell survival, growth and invasion. [provided by RefSeq, Jul 2016].
Transcript (Including UTRs)
   Position: hg19 chr19:57,862,645-57,871,265 Size: 8,621 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr19:57,863,033-57,869,217 Size: 6,185 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 (chr19:57,862,645-57,871,265)mRNA (may differ from genome)Protein (659 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ZN304_HUMAN
DESCRIPTION: RecName: Full=Zinc finger protein 304;
FUNCTION: May be involved in transcriptional regulation.
SUBCELLULAR LOCATION: Nucleus (Probable).
SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein family.
SIMILARITY: Contains 16 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: 7.55 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 155.97 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 -151.02388-0.389 Picture PostScript Text
3' UTR -630.022048-0.308 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
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 Q9HCX3
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:0005515 protein binding
GO:0046872 metal ion binding
GO:1990841 promoter-specific chromatin binding

Biological Process:
GO:0001525 angiogenesis
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007229 integrin-mediated signaling pathway
GO:0007265 Ras protein signal transduction
GO:0030335 positive regulation of cell migration
GO:0035562 negative regulation of chromatin binding
GO:0045766 positive regulation of angiogenesis
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0050679 positive regulation of epithelial cell proliferation
GO:0090309 positive regulation of methylation-dependent chromatin silencing
GO:1900114 positive regulation of histone H3-K9 trimethylation
GO:1902466 positive regulation of histone H3-K27 trimethylation
GO:2000811 negative regulation of anoikis

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AJ276316 - Homo sapiens mRNA for zinc finger protein (ZNF304 gene).
BC111531 - Homo sapiens zinc finger protein 304, mRNA (cDNA clone MGC:129703 IMAGE:40012297), complete cds.
BC111532 - Homo sapiens zinc finger protein 304, mRNA (cDNA clone MGC:129704 IMAGE:40012300), complete cds.
JD051414 - Sequence 32438 from Patent EP1572962.
JD154252 - Sequence 135276 from Patent EP1572962.
JD552451 - Sequence 533475 from Patent EP1572962.
JD191833 - Sequence 172857 from Patent EP1572962.
JD180056 - Sequence 161080 from Patent EP1572962.
JD289280 - Sequence 270304 from Patent EP1572962.
AB527707 - Synthetic construct DNA, clone: pF1KB6190, Homo sapiens ZNF304 gene for zinc finger protein 304, without stop codon, in Flexi system.
EU446832 - Synthetic construct Homo sapiens clone IMAGE:100070313; IMAGE:100012041; FLH257262.01L zinc finger protein 304 (ZNF304) gene, encodes complete protein.
JD314815 - Sequence 295839 from Patent EP1572962.
JD288454 - Sequence 269478 from Patent EP1572962.
JD247572 - Sequence 228596 from Patent EP1572962.
JD283677 - Sequence 264701 from Patent EP1572962.
JD147678 - Sequence 128702 from Patent EP1572962.
JD214649 - Sequence 195673 from Patent EP1572962.
JD186209 - Sequence 167233 from Patent EP1572962.
JD290605 - Sequence 271629 from Patent EP1572962.
JD351634 - Sequence 332658 from Patent EP1572962.
JD468286 - Sequence 449310 from Patent EP1572962.
JD208098 - Sequence 189122 from Patent EP1572962.
JD427639 - Sequence 408663 from Patent EP1572962.
JD063503 - Sequence 44527 from Patent EP1572962.
JD221018 - Sequence 202042 from Patent EP1572962.
JD368977 - Sequence 350001 from Patent EP1572962.
JD460502 - Sequence 441526 from Patent EP1572962.
JD048168 - Sequence 29192 from Patent EP1572962.
JD492237 - Sequence 473261 from Patent EP1572962.
JD052324 - Sequence 33348 from Patent EP1572962.
JD109463 - Sequence 90487 from Patent EP1572962.
JD277871 - Sequence 258895 from Patent EP1572962.
JD155624 - Sequence 136648 from Patent EP1572962.
JD450982 - Sequence 432006 from Patent EP1572962.
JD383322 - Sequence 364346 from Patent EP1572962.
JD410404 - Sequence 391428 from Patent EP1572962.
JD305998 - Sequence 287022 from Patent EP1572962.
JD177803 - Sequence 158827 from Patent EP1572962.
JD566637 - Sequence 547661 from Patent EP1572962.
JD509122 - Sequence 490146 from Patent EP1572962.
JD556996 - Sequence 538020 from Patent EP1572962.
JD236642 - Sequence 217666 from Patent EP1572962.

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

Protein Q9HCX3 (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: NM_020657, NP_065708, Q9HCX3, ZN304_HUMAN
UCSC ID: uc010ygw.2
RefSeq Accession: NM_020657
Protein: Q9HCX3 (aka ZN304_HUMAN or Z304_HUMAN)
CCDS: CCDS12950.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_020657.2
exon count: 3CDS single in 3' UTR: no RNA size: 4417
ORF size: 1980CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4073.00frame shift in genome: no % Coverage: 99.98
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.