Human Gene ZNF397 (uc010dmp.3) Description and Page Index
  Description: Homo sapiens zinc finger protein 397 (ZNF397), transcript variant 1, mRNA.
RefSeq Summary (NM_001135178): This gene encodes a protein with a N-terminal SCAN domain, and the longer isoform contains nine C2H2-type zinc finger repeats in the C-terminal domain. The protein localizes to centromeres during interphase and early prophase, and different isoforms can repress or activate transcription in transfection studies. Multiple transcript variants encoding different isoforms have been found for this gene. Additional variants have been described, but their biological validity has not been determined. [provided by RefSeq, Oct 2009].
Transcript (Including UTRs)
   Position: hg19 chr18:32,820,994-32,827,153 Size: 6,160 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr18:32,822,435-32,826,274 Size: 3,840 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr18:32,820,994-32,827,153)mRNA (may differ from genome)Protein (534 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Zinc finger protein 397; AltName: Full=Zinc finger and SCAN domain-containing protein 15; AltName: Full=Zinc finger protein 47;
FUNCTION: Isoform 3 acts as a DNA-dependent transcriptional repressor.
SUBUNIT: Isoforms 1 and 3 can both homo- and hetero-associate. Homo-association of isoform 1 is dependent on the presence of the SCAN domain.
SUBCELLULAR LOCATION: Isoform 3: Nucleus. Cytoplasm.
TISSUE SPECIFICITY: Expressed strongly in testis, moderately in skeletal muscle, pancreas and prostate, and weakly in heart, placenta, liver, kidney, spleen, thymus and small intestine.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein family.
SIMILARITY: Contains 9 C2H2-type zinc fingers.
SIMILARITY: Contains 1 SCAN box domain.

-  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: 4.74 RPKM in Ovary
Total median expression: 148.91 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 -54.20160-0.339 Picture PostScript Text
3' UTR -253.30879-0.288 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
IPR008916 - Retrov_capsid_C
IPR003309 - Tscrpt_reg_SCAN
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

Pfam Domains:
PF00096 - Zinc finger, C2H2 type
PF02023 - SCAN domain
PF13894 - C2H2-type zinc finger
PF13912 - C2H2-type zinc finger

SCOP Domains:
48695 - Multiheme cytochromes
57667 - C2H2 and C2HC zinc fingers

ModBase Predicted Comparative 3D Structure on Q8NF99
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     
Gene Sorter     

-  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:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0015630 microtubule cytoskeleton

-  Descriptions from all associated GenBank mRNAs
  AK027384 - Homo sapiens cDNA FLJ14478 fis, clone MAMMA1001633, moderately similar to ZINC FINGER PROTEIN 165.
AY157641 - Homo sapiens zinc finger protein 397 truncated isoform (ZNF397) mRNA, complete cds.
AF533250 - Homo sapiens zinc finger protein (ZNF397) mRNA, complete cds.
AK311533 - Homo sapiens cDNA, FLJ18575.
BC006172 - Homo sapiens zinc finger protein 397, mRNA (cDNA clone MGC:13250 IMAGE:4053312), complete cds.
JD220511 - Sequence 201535 from Patent EP1572962.
JD478713 - Sequence 459737 from Patent EP1572962.
JD522690 - Sequence 503714 from Patent EP1572962.
KJ894976 - Synthetic construct Homo sapiens clone ccsbBroadEn_04370 ZNF397 gene, encodes complete protein.
EU446677 - Synthetic construct Homo sapiens clone IMAGE:100070151; IMAGE:100011886; FLH258166.01L zinc finger protein 397 (ZNF397) gene, encodes complete protein.
DQ588954 - Homo sapiens piRNA piR-56066, complete sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001135178, NP_001128650, Q8NF99, Q9BRM2, ZN397_HUMAN, ZNF47, ZSCAN15
UCSC ID: uc010dmp.3
RefSeq Accession: NM_001135178
Protein: Q8NF99 (aka ZN397_HUMAN or Z397_HUMAN)
CCDS: CCDS45852.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001135178.2
exon count: 4CDS single in 3' UTR: no RNA size: 2644
ORF size: 1605CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3407.00frame shift in genome: no % Coverage: 100.00
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: 1838# 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.