Human Gene ZNF568 (uc002ofc.3) Description and Page Index
  Description: Homo sapiens zinc finger protein 568 (ZNF568), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr19:37,407,231-37,443,645 Size: 36,415 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr19:37,413,673-37,441,990 Size: 28,318 Coding Exon Count: 5 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:37,407,231-37,443,645)mRNA (may differ from genome)Protein (644 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: ZN568_HUMAN
DESCRIPTION: RecName: Full=Zinc finger protein 568;
FUNCTION: May be involved in transcriptional regulation (By similarity).
SUBCELLULAR LOCATION: Nucleus (Probable).
SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein family.
SIMILARITY: Contains 15 C2H2-type zinc fingers.
SIMILARITY: Contains 1 KRAB domain.
SEQUENCE CAUTION: Sequence=AAH31218.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAH31218.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=CAE45810.1; Type=Frameshift; Positions=436;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ZNF568
CDC HuGE Published Literature: ZNF568
Positive Disease Associations: Breath Tests , Cholesterol, HDL
Related Studies:
  1. Breath Tests
    , , . [PubMed 0]
  2. Cholesterol, HDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  3. Cholesterol, HDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
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-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 2.06 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 53.17 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -202.11518-0.390 Picture PostScript Text
3' UTR -455.621655-0.275 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 Q3ZCX4
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 Details     
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000976 transcription regulatory region sequence-specific DNA binding
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:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001701 in utero embryonic development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0045892 negative regulation of transcription, DNA-templated
GO:0060669 embryonic placenta morphogenesis

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC108696 - Homo sapiens cDNA clone IMAGE:3873246.
AK299626 - Homo sapiens cDNA FLJ57578 complete cds, moderately similar to Mus musculus zinc finger protein 568 (Zfp568), mRNA.
BC016334 - Homo sapiens zinc finger protein 568, mRNA (cDNA clone IMAGE:4052822), partial cds.
BC031218 - Homo sapiens zinc finger protein 568, mRNA (cDNA clone IMAGE:4811402), partial cds.
BX640681 - Homo sapiens mRNA; cDNA DKFZp686B0797 (from clone DKFZp686B0797).
AK093123 - Homo sapiens cDNA FLJ35804 fis, clone TESTI2005981, moderately similar to ZINC FINGER PROTEIN 84.
AX747939 - Sequence 1464 from Patent EP1308459.
BC131547 - Homo sapiens zinc finger protein 568, mRNA (cDNA clone IMAGE:40032834), partial cds.
BC111777 - Homo sapiens zinc finger protein 568, mRNA (cDNA clone IMAGE:40032833).
JD311608 - Sequence 292632 from Patent EP1572962.
JD081439 - Sequence 62463 from Patent EP1572962.
JD314899 - Sequence 295923 from Patent EP1572962.
JD314900 - Sequence 295924 from Patent EP1572962.
JD314898 - Sequence 295922 from Patent EP1572962.
JD314885 - Sequence 295909 from Patent EP1572962.
JD314816 - Sequence 295840 from Patent EP1572962.
JD314817 - Sequence 295841 from Patent EP1572962.
JD316290 - Sequence 297314 from Patent EP1572962.
JD032199 - Sequence 13223 from Patent EP1572962.
JD314885 - Sequence 295909 from Patent EP1572962.
JD032199 - Sequence 13223 from Patent EP1572962.
JD314816 - Sequence 295840 from Patent EP1572962.
JD314817 - Sequence 295841 from Patent EP1572962.
JD434463 - Sequence 415487 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.

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

Protein Q3ZCX4 (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_198539, NP_001191766, Q3ZCX4, Q6N060, Q8NA64, ZN568_HUMAN
UCSC ID: uc002ofc.3
RefSeq Accession: NM_198539
Protein: Q3ZCX4 (aka ZN568_HUMAN)
CCDS: CCDS42558.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_198539.3
exon count: 7CDS single in 3' UTR: no RNA size: 4125
ORF size: 1935CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3765.00frame shift in genome: no % Coverage: 99.59
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.