Human Gene ZNF398 (ENST00000475153.6) from GENCODE V44
  Description: Homo sapiens zinc finger protein 398 (ZNF398), transcript variant 1, mRNA. (from RefSeq NM_170686)
RefSeq Summary (NM_170686): This gene encodes a member of the Kruppel family of C2H2-type zinc-finger transcription factor proteins. The encoded protein acts as a transcriptional activator. Two transcript variants encoding distinct isoforms have been identified for this gene. Other transcript variants have been described, but their full length sequence has not been determined. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000475153.6
Gencode Gene: ENSG00000197024.9
Transcript (Including UTRs)
   Position: hg38 chr7:149,147,453-149,183,042 Size: 35,590 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg38 chr7:149,147,743-149,179,801 Size: 32,059 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:149,147,453-149,183,042)mRNA (may differ from genome)Protein (642 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ZN398_HUMAN
DESCRIPTION: RecName: Full=Zinc finger protein 398; AltName: Full=Zinc finger DNA-binding protein p52/p71;
FUNCTION: Function as a transcriptional activator.
SUBCELLULAR LOCATION: Nucleus (Probable).
INDUCTION: By estrogen receptor alpha.
SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein family.
SIMILARITY: Contains 9 C2H2-type zinc fingers.
SIMILARITY: Contains 1 KRAB domain.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: ZNF398
Diseases sorted by gene-association score: microphthalmia with limb anomalies (2), aleutian mink disease (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.63 RPKM in Testis
Total median expression: 133.41 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 -160.60290-0.554 Picture PostScript Text
3' UTR -933.903241-0.288 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
IPR022137 - DUF3669_Znf
IPR001909 - Krueppel-associated_box
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

Pfam Domains:
PF12417 - Zinc finger protein
PF01352 - KRAB box

ModBase Predicted Comparative 3D Structure on Q8TD17
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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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  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:0005515 protein 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
GO:0045893 positive regulation of transcription, DNA-templated

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AY049743 - Homo sapiens zinc finger DNA binding protein p52 (ZER6) mRNA, complete cds, alternatively spliced.
LF384105 - JP 2014500723-A/191608: Polycomb-Associated Non-Coding RNAs.
MA619682 - JP 2018138019-A/191608: Polycomb-Associated Non-Coding RNAs.
AK026380 - Homo sapiens cDNA: FLJ22727 fis, clone HSI15054.
BC043295 - Homo sapiens zinc finger protein 398, mRNA (cDNA clone MGC:44469 IMAGE:5298104), complete cds.
AK290499 - Homo sapiens cDNA FLJ76783 complete cds, highly similar to Homo sapiens zinc finger protein 398 (ZNF398), transcript variant 1, mRNA.
AY049744 - Homo sapiens zinc finger DNA binding protein p71 (ZER6) mRNA, complete cds, alternatively spliced.
AB527270 - Synthetic construct DNA, clone: pF1KA1339, Homo sapiens ZNF398 gene for zinc finger protein 398, without stop codon, in Flexi system.
CU692152 - Synthetic construct Homo sapiens gateway clone IMAGE:100020949 5' read ZNF398 mRNA.
KJ899348 - Synthetic construct Homo sapiens clone ccsbBroadEn_08742 ZNF398 gene, encodes complete protein.
AK301890 - Homo sapiens cDNA FLJ59779 complete cds, highly similar to Zinc finger protein 398.
JD201557 - Sequence 182581 from Patent EP1572962.
JD226586 - Sequence 207610 from Patent EP1572962.
JD111566 - Sequence 92590 from Patent EP1572962.
JD510568 - Sequence 491592 from Patent EP1572962.
JD322757 - Sequence 303781 from Patent EP1572962.
JD108334 - Sequence 89358 from Patent EP1572962.
JD214924 - Sequence 195948 from Patent EP1572962.
JD240423 - Sequence 221447 from Patent EP1572962.
AK304603 - Homo sapiens cDNA FLJ50379 complete cds, highly similar to Zinc finger protein 398.
JD564785 - Sequence 545809 from Patent EP1572962.
JD251511 - Sequence 232535 from Patent EP1572962.
JD386155 - Sequence 367179 from Patent EP1572962.
JD352228 - Sequence 333252 from Patent EP1572962.
AK304369 - Homo sapiens cDNA FLJ50366 complete cds, highly similar to Zinc finger protein 398.
LF362174 - JP 2014500723-A/169677: Polycomb-Associated Non-Coding RNAs.
MA597751 - JP 2018138019-A/169677: Polycomb-Associated Non-Coding RNAs.
AB037760 - Homo sapiens mRNA for KIAA1339 protein, partial cds.
JD280152 - Sequence 261176 from Patent EP1572962.
JD237985 - Sequence 219009 from Patent EP1572962.
JD273730 - Sequence 254754 from Patent EP1572962.
JD343530 - Sequence 324554 from Patent EP1572962.
JD101554 - Sequence 82578 from Patent EP1572962.
JD504368 - Sequence 485392 from Patent EP1572962.
JD386784 - Sequence 367808 from Patent EP1572962.
JD333411 - Sequence 314435 from Patent EP1572962.
JD368352 - Sequence 349376 from Patent EP1572962.
JD301734 - Sequence 282758 from Patent EP1572962.
JD545387 - Sequence 526411 from Patent EP1572962.
JD508782 - Sequence 489806 from Patent EP1572962.
JD182359 - Sequence 163383 from Patent EP1572962.
JD332765 - Sequence 313789 from Patent EP1572962.
JD521675 - Sequence 502699 from Patent EP1572962.
JD455918 - Sequence 436942 from Patent EP1572962.
JD470014 - Sequence 451038 from Patent EP1572962.
JD507100 - Sequence 488124 from Patent EP1572962.
JD288401 - Sequence 269425 from Patent EP1572962.
JD496262 - Sequence 477286 from Patent EP1572962.
JD291206 - Sequence 272230 from Patent EP1572962.
JD305683 - Sequence 286707 from Patent EP1572962.
JD146662 - Sequence 127686 from Patent EP1572962.
JD251832 - Sequence 232856 from Patent EP1572962.
JD495822 - Sequence 476846 from Patent EP1572962.
JD081903 - Sequence 62927 from Patent EP1572962.
LF362176 - JP 2014500723-A/169679: Polycomb-Associated Non-Coding RNAs.
MA597753 - JP 2018138019-A/169679: Polycomb-Associated Non-Coding RNAs.
JD553437 - Sequence 534461 from Patent EP1572962.
JD136815 - Sequence 117839 from Patent EP1572962.
JD042220 - Sequence 23244 from Patent EP1572962.
JD171774 - Sequence 152798 from Patent EP1572962.
JD044876 - Sequence 25900 from Patent EP1572962.
JD511379 - Sequence 492403 from Patent EP1572962.
JD090770 - Sequence 71794 from Patent EP1572962.
JD126580 - Sequence 107604 from Patent EP1572962.
JD435634 - Sequence 416658 from Patent EP1572962.
JD276817 - Sequence 257841 from Patent EP1572962.
JD094740 - Sequence 75764 from Patent EP1572962.
JD282620 - Sequence 263644 from Patent EP1572962.
JD330505 - Sequence 311529 from Patent EP1572962.
JD295831 - Sequence 276855 from Patent EP1572962.
JD310978 - Sequence 292002 from Patent EP1572962.
JD309125 - Sequence 290149 from Patent EP1572962.
JD563625 - Sequence 544649 from Patent EP1572962.
JD312866 - Sequence 293890 from Patent EP1572962.
JD223767 - Sequence 204791 from Patent EP1572962.
JD183184 - Sequence 164208 from Patent EP1572962.
LF362177 - JP 2014500723-A/169680: Polycomb-Associated Non-Coding RNAs.
MA597754 - JP 2018138019-A/169680: Polycomb-Associated Non-Coding RNAs.

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

Protein Q8TD17 (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: A8K384, B4E377, ENST00000475153.1, ENST00000475153.2, ENST00000475153.3, ENST00000475153.4, ENST00000475153.5, KIAA1339, NM_170686, Q8TD17, Q8TD18, Q9P2K7, Q9UDV8, uc003wfl.1, uc003wfl.2, uc003wfl.3, uc003wfl.4, uc003wfl.5, ZER6, ZN398_HUMAN
UCSC ID: ENST00000475153.6
RefSeq Accession: NM_170686
Protein: Q8TD17 (aka ZN398_HUMAN or Z398_HUMAN)
CCDS: CCDS5894.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.