Human Gene ZNF678 (uc021pjy.1)
  Description: Homo sapiens zinc finger protein 678 (ZNF678), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:227,751,220-227,850,164 Size: 98,945 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr1:227,751,396-227,843,529 Size: 92,134 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:227,751,220-227,850,164)mRNA (may differ from genome)Protein (580 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIPubMed
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F5GXA7_HUMAN
DESCRIPTION: SubName: Full=Zinc finger protein 678;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ZNF678
CDC HuGE Published Literature: ZNF678
Positive Disease Associations: Body Height , height
Related Studies:
  1. Body Height
    Michael N Weedon et al. Nature genetics 2008, Genome-wide association analysis identifies 20 loci that influence adult height., Nature genetics. [PubMed 18391952]
  2. height
    Weedon ,et al. 2008, Genome-wide association analysis identifies 20 loci that influence adult height, Nature genetics 2008 40- 5 : 575-83. [PubMed 18391952]

-  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: 1.65 RPKM in Prostate
Total median expression: 44.82 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 -74.02176-0.421 Picture PostScript Text
3' UTR -1630.806635-0.246 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 F5GXA7
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
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK026475 - Homo sapiens cDNA: FLJ22822 fis, clone KAIA3968.
BC042500 - Homo sapiens zinc finger protein 678, mRNA (cDNA clone MGC:42493 IMAGE:4823179), complete cds.
AK307248 - Homo sapiens cDNA, FLJ97196.
AK311313 - Homo sapiens cDNA, FLJ18355.
JD103622 - Sequence 84646 from Patent EP1572962.
JD566198 - Sequence 547222 from Patent EP1572962.
JD142971 - Sequence 123995 from Patent EP1572962.
JD085960 - Sequence 66984 from Patent EP1572962.
JD135464 - Sequence 116488 from Patent EP1572962.
KJ905081 - Synthetic construct Homo sapiens clone ccsbBroadEn_14475 ZNF678-like gene, encodes complete protein.
JD314882 - Sequence 295906 from Patent EP1572962.
JD240527 - Sequence 221551 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.
JD314888 - Sequence 295912 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.
JD314877 - Sequence 295901 from Patent EP1572962.
JD314878 - Sequence 295902 from Patent EP1572962.
LF340536 - JP 2014500723-A/148039: Polycomb-Associated Non-Coding RNAs.
JD330509 - Sequence 311533 from Patent EP1572962.
JD330511 - Sequence 311535 from Patent EP1572962.
JD330510 - Sequence 311534 from Patent EP1572962.
DQ570709 - Homo sapiens piRNA piR-30821, complete sequence.
JD037677 - Sequence 18701 from Patent EP1572962.
JD314875 - Sequence 295899 from Patent EP1572962.
JD314879 - Sequence 295903 from Patent EP1572962.
JD314877 - Sequence 295901 from Patent EP1572962.
JD314878 - Sequence 295902 from Patent EP1572962.
LF340536 - JP 2014500723-A/148039: Polycomb-Associated Non-Coding RNAs.
JD330509 - Sequence 311533 from Patent EP1572962.
JD330511 - Sequence 311535 from Patent EP1572962.
JD330510 - Sequence 311534 from Patent EP1572962.
DQ570709 - Homo sapiens piRNA piR-30821, complete sequence.
JD037677 - Sequence 18701 from Patent EP1572962.
JD314879 - Sequence 295903 from Patent EP1572962.
JD314877 - Sequence 295901 from Patent EP1572962.
JD314878 - Sequence 295902 from Patent EP1572962.
DQ570709 - Homo sapiens piRNA piR-30821, complete sequence.
JD314879 - Sequence 295903 from Patent EP1572962.
JD314877 - Sequence 295901 from Patent EP1572962.
JD314878 - Sequence 295902 from Patent EP1572962.
JD330509 - Sequence 311533 from Patent EP1572962.
JD330511 - Sequence 311535 from Patent EP1572962.
JD330510 - Sequence 311534 from Patent EP1572962.
DQ570709 - Homo sapiens piRNA piR-30821, complete sequence.
JD037677 - Sequence 18701 from Patent EP1572962.
JD314877 - Sequence 295901 from Patent EP1572962.
JD314878 - Sequence 295902 from Patent EP1572962.
JD314879 - Sequence 295903 from Patent EP1572962.
JD314881 - Sequence 295905 from Patent EP1572962.
JD110081 - Sequence 91105 from Patent EP1572962.
JD038263 - Sequence 19287 from Patent EP1572962.
JD240557 - Sequence 221581 from Patent EP1572962.
JD101145 - Sequence 82169 from Patent EP1572962.
JD494777 - Sequence 475801 from Patent EP1572962.
AB074269 - Homo sapiens primary neuroblastoma cDNA, clone:Nbla10712, full insert sequence.
JD019348 - Sequence 372 from Patent EP1572962.
JD033790 - Sequence 14814 from Patent EP1572962.
BC007286 - Homo sapiens cDNA clone IMAGE:3344302.
JD383175 - Sequence 364199 from Patent EP1572962.
JD092777 - Sequence 73801 from Patent EP1572962.
JD442669 - Sequence 423693 from Patent EP1572962.
KJ904195 - Synthetic construct Homo sapiens clone ccsbBroadEn_13589 ZNF678 gene, encodes complete protein.
JD514731 - Sequence 495755 from Patent EP1572962.
JD040003 - Sequence 21027 from Patent EP1572962.
JD317285 - Sequence 298309 from Patent EP1572962.
JD117984 - Sequence 99008 from Patent EP1572962.
JD433765 - Sequence 414789 from Patent EP1572962.
JD307616 - Sequence 288640 from Patent EP1572962.
JD058278 - Sequence 39302 from Patent EP1572962.
JD112833 - Sequence 93857 from Patent EP1572962.
MA576113 - JP 2018138019-A/148039: Polycomb-Associated Non-Coding RNAs.
MA576113 - JP 2018138019-A/148039: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: F5GXA7, F5GXA7_HUMAN, NM_178549, NP_848644
UCSC ID: uc021pjy.1
RefSeq Accession: NM_178549
Protein: F5GXA7

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_178549.3
exon count: 4CDS single in 3' UTR: no RNA size: 8565
ORF size: 1743CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3470.00frame shift in genome: no % Coverage: 99.87
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: 7987# 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.