Human Gene ZNF680 (uc003tta.1)
  Description: zinc finger protein 680 isoform 1
Transcript (Including UTRs)
   Position: hg18 chr7:63,617,697-63,660,919 Size: 43,223 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg18 chr7:63,618,974-63,660,767 Size: 41,794 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated at UCSC: 2009-03-03

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:63,617,697-63,660,919)mRNA (may differ from genome)Protein (530 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDMGIPubMedReactome
TreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ZN680_HUMAN
DESCRIPTION: RecName: Full=Zinc finger protein 680;
FUNCTION: May be involved in transcriptional regulation.
SUBCELLULAR LOCATION: Nucleus (Probable).
SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein family.
SIMILARITY: Contains 12 C2H2-type zinc fingers.
SIMILARITY: Contains 1 KRAB domain.
SEQUENCE CAUTION: Sequence=BAC11286.1; Type=Erroneous initiation;

-  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

-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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Affymetrix All Exon Microarrays

           
Ratios

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -51.90152-0.341 Picture PostScript Text
3' UTR -271.961277-0.213 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

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 Q8NEM1
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 orthologGenome Browser
     Gene Details
     Gene Sorter
     SGD
     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:0003676 nucleic acid binding
GO:0003677 DNA 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:0005622 intracellular
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  L32135 - Homo sapiens (clone tec221) mRNA.
X79013 - H.sapiens clone tec221 mRNA polyA signal (expressed in Tera-2 clone13).
AK074911 - Homo sapiens cDNA FLJ90430 fis, clone NT2RP3000652, moderately similar to ZINC FINGER PROTEIN 43.
AK122937 - Homo sapiens cDNA FLJ16633 fis, clone TESTI4024740, highly similar to Zinc finger protein 680.
BC030700 - Homo sapiens zinc finger protein 680, mRNA (cDNA clone MGC:26916 IMAGE:4837196), complete cds.
EU832109 - Synthetic construct Homo sapiens clone HAIB:100067138; DKFZo008B1125 zinc finger protein 680 protein (ZNF680) gene, encodes complete protein.
EU832203 - Synthetic construct Homo sapiens clone HAIB:100067232; DKFZo004B1126 zinc finger protein 680 protein (ZNF680) gene, encodes complete protein.
AB529206 - Synthetic construct DNA, clone: pF1KB9044, Homo sapiens ZNF680 gene for zinc finger protein 680, without stop codon, in Flexi system.
AK131240 - Homo sapiens cDNA FLJ16156 fis, clone BRAWH2006207, moderately similar to Zinc finger protein 91.
AK094476 - Homo sapiens cDNA FLJ37157 fis, clone BRACE2026142.
JF432724 - Synthetic construct Homo sapiens clone IMAGE:100073966 zinc finger protein 680 (ZNF680) gene, encodes complete protein.
DQ570709 - Homo sapiens piRNA piR-30821, complete sequence.
DQ570709 - Homo sapiens piRNA piR-30821, complete sequence.
JD530272 - Sequence 511296 from Patent EP1572962.
JD381503 - Sequence 362527 from Patent EP1572962.
JD423637 - Sequence 404661 from Patent EP1572962.
KJ900630 - Synthetic construct Homo sapiens clone ccsbBroadEn_10024 ZNF680 gene, encodes complete protein.
JD314886 - Sequence 295910 from Patent EP1572962.
JD314887 - Sequence 295911 from Patent EP1572962.
JD314877 - Sequence 295901 from Patent EP1572962.
JD314878 - Sequence 295902 from Patent EP1572962.
JD314879 - Sequence 295903 from Patent EP1572962.
JD314877 - Sequence 295901 from Patent EP1572962.
JD314878 - Sequence 295902 from Patent EP1572962.
JD314879 - Sequence 295903 from Patent EP1572962.
JD314877 - Sequence 295901 from Patent EP1572962.
JD314878 - Sequence 295902 from Patent EP1572962.
JD314879 - Sequence 295903 from Patent EP1572962.
JD305295 - Sequence 286319 from Patent EP1572962.
JD291876 - Sequence 272900 from Patent EP1572962.
JD314768 - Sequence 295792 from Patent EP1572962.
JD037677 - Sequence 18701 from Patent EP1572962.
JD330510 - Sequence 311534 from Patent EP1572962.
JD330511 - Sequence 311535 from Patent EP1572962.
JD330509 - Sequence 311533 from Patent EP1572962.
JD037677 - Sequence 18701 from Patent EP1572962.
JD330510 - Sequence 311534 from Patent EP1572962.
JD330511 - Sequence 311535 from Patent EP1572962.
JD330509 - Sequence 311533 from Patent EP1572962.
JD037677 - Sequence 18701 from Patent EP1572962.
JD330510 - Sequence 311534 from Patent EP1572962.
JD330511 - Sequence 311535 from Patent EP1572962.
JD330509 - Sequence 311533 from Patent EP1572962.
JD259381 - Sequence 240405 from Patent EP1572962.
JD259380 - Sequence 240404 from Patent EP1572962.
JD105237 - Sequence 86261 from Patent EP1572962.
LF340536 - JP 2014500723-A/148039: Polycomb-Associated Non-Coding RNAs.
LF340536 - JP 2014500723-A/148039: Polycomb-Associated Non-Coding RNAs.
MA576113 - JP 2018138019-A/148039: Polycomb-Associated Non-Coding RNAs.
MA576113 - JP 2018138019-A/148039: Polycomb-Associated Non-Coding RNAs.

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

Protein Q8NEM1 (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_178558, NP_848653, Q8NC79, Q8NEM1, ZN680_HUMAN
UCSC ID: uc003tta.1
RefSeq Accession: NM_178558
Protein: Q8NEM1 (aka ZN680_HUMAN)
CCDS: CCDS34644.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_178558.3
exon count: 4CDS single in 3' UTR: no RNA size: 3041
ORF size: 1593CDS single in intron: no Alignment % ID: 99.83
txCdsPredict score: 2347.50frame shift in genome: no % Coverage: 99.38
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.