Human Gene ZCCHC3 (ENST00000500893.4_5) from GENCODE V47lift37
  Description: zinc finger CCHC-type containing 3 (from RefSeq NM_033089.7)
Gencode Transcript: ENST00000500893.4_5
Gencode Gene: ENSG00000247315.4_8
Transcript (Including UTRs)
   Position: hg19 chr20:278,211-280,965 Size: 2,755 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr20:278,228-279,442 Size: 1,215 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:278,211-280,965)mRNA (may differ from genome)Protein (404 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ZCHC3_HUMAN
DESCRIPTION: RecName: Full=Zinc finger CCHC domain-containing protein 3;
SIMILARITY: Contains 3 CCHC-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: 20.26 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 448.62 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 -0.2017-0.012 Picture PostScript Text
3' UTR -442.201523-0.290 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
IPR001878 - Znf_CCHC

Pfam Domains:
PF00098 - Zinc knuckle
PF14392 - Zinc knuckle

SCOP Domains:
57756 - Retrovirus zinc finger-like domains

ModBase Predicted Comparative 3D Structure on Q9NUD5
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding


-  Descriptions from all associated GenBank mRNAs
  BC020460 - Homo sapiens zinc finger, CCHC domain containing 3, mRNA (cDNA clone IMAGE:4456008).
LF205955 - JP 2014500723-A/13458: Polycomb-Associated Non-Coding RNAs.
BC069238 - Homo sapiens zinc finger, CCHC domain containing 3, mRNA (cDNA clone MGC:78475 IMAGE:6287290), complete cds.
AK025768 - Homo sapiens cDNA: FLJ22115 fis, clone HEP18471.
BC107584 - Homo sapiens zinc finger, CCHC domain containing 3, mRNA (cDNA clone MGC:104290 IMAGE:6457775), complete cds.
BC036469 - Homo sapiens zinc finger, CCHC domain containing 3, mRNA (cDNA clone IMAGE:5261152), with apparent retained intron.
LF350125 - JP 2014500723-A/157628: Polycomb-Associated Non-Coding RNAs.
LF350124 - JP 2014500723-A/157627: Polycomb-Associated Non-Coding RNAs.
LF350123 - JP 2014500723-A/157626: Polycomb-Associated Non-Coding RNAs.
LF350122 - JP 2014500723-A/157625: Polycomb-Associated Non-Coding RNAs.
JD483064 - Sequence 464088 from Patent EP1572962.
JD510464 - Sequence 491488 from Patent EP1572962.
JD287891 - Sequence 268915 from Patent EP1572962.
JD559216 - Sequence 540240 from Patent EP1572962.
JD484641 - Sequence 465665 from Patent EP1572962.
LF350119 - JP 2014500723-A/157622: Polycomb-Associated Non-Coding RNAs.
JD190077 - Sequence 171101 from Patent EP1572962.
JD105018 - Sequence 86042 from Patent EP1572962.
JD253625 - Sequence 234649 from Patent EP1572962.
JD285630 - Sequence 266654 from Patent EP1572962.
JD155341 - Sequence 136365 from Patent EP1572962.
LF350118 - JP 2014500723-A/157621: Polycomb-Associated Non-Coding RNAs.
JD565197 - Sequence 546221 from Patent EP1572962.
MA585702 - JP 2018138019-A/157628: Polycomb-Associated Non-Coding RNAs.
MA585701 - JP 2018138019-A/157627: Polycomb-Associated Non-Coding RNAs.
MA585700 - JP 2018138019-A/157626: Polycomb-Associated Non-Coding RNAs.
MA585699 - JP 2018138019-A/157625: Polycomb-Associated Non-Coding RNAs.
MA585696 - JP 2018138019-A/157622: Polycomb-Associated Non-Coding RNAs.
MA585695 - JP 2018138019-A/157621: Polycomb-Associated Non-Coding RNAs.
MA441532 - JP 2018138019-A/13458: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: C20orf99 , ENST00000500893.1, ENST00000500893.2, ENST00000500893.3, NM_033089, Q3B7J3, Q6NT79, Q9NUD5, uc322vlf.1, uc322vlf.2, ZCCHC3 , ZCHC3_HUMAN
UCSC ID: ENST00000500893.4_5
RefSeq Accession: NM_033089.7
Protein: Q9NUD5 (aka ZCHC3_HUMAN or ZCH3_HUMAN)

-  Gene Model Information
  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.