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Aliases for ZNF90 Gene

Aliases for ZNF90 Gene

  • Zinc Finger Protein 90 2 3 5
  • Zinc Finger Protein HTF9 3 4
  • Zinc Finger Protein 90 (HTF9) 2
  • HTF9 3

External Ids for ZNF90 Gene

Previous GeneCards Identifiers for ZNF90 Gene

  • GC19P020725
  • GC19P020580
  • GC19P020034
  • GC19P020073
  • GC19P020049
  • GC19P020076
  • GC19U900566
  • GC19P019977
  • GC19P020188
  • GC19P020079

Summaries for ZNF90 Gene

GeneCards Summary for ZNF90 Gene

ZNF90 (Zinc Finger Protein 90) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and structural constituent of ribosome. An important paralog of this gene is ZNF66.

UniProtKB/Swiss-Prot for ZNF90 Gene

  • May be involved in transcriptional regulation.

Additional gene information for ZNF90 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZNF90 Gene

Genomics for ZNF90 Gene

GeneHancer (GH) Regulatory Elements for ZNF90 Gene

Promoters and enhancers for ZNF90 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I020077 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 550.8 +2.7 2720 6.8 TFAP4 MXI1 PKNOX1 USF1 SAP130 ARID4B MAX ZSCAN9 YY1 GATAD1 ZNF90 LOC100419301 ZNF682 BNIP3P15 CILP2 MEF2B ZNF506 BNIP3P14
GH19I019374 Enhancer 1.2 Ensembl ENCODE dbSUPER 66.9 -702.8 -702831 0.9 ZNF493 MZF1 ZBTB40 ZNF155 ZNF213 ZNF354C ZNF138 SCRT2 KLF7 ZNF202 NR2C2AP ATP13A1 ENSG00000268030 ENSG00000267481 ZNF90 UPF1 ZNF253 MAU2 SUGP2 ENSG00000268938
GH19I021019 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 19.5 +944.3 944282 4.6 HDGF PKNOX1 ATF1 SMAD1 ARID4B SIN3A DMAP1 YY1 POLR2B ZNF207 ZNF430 ZNF100 LOC641367 ZNF714 ZNF90 BNIP3P26 RPL7AP10 ZNF66 ZNF431 ZNF486
GH19I019899 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 16.2 -176.8 -176836 3 PKNOX1 ATF1 FOXA2 SIN3A ZNF2 YY1 GTF3C2 TCF12 POLR2B ZNF766 ZNF93 ATP13A1 ZNF90 ZNF506 NR2C2AP ENSG00000267481 TMEM161A ZNF66 MAU2 ZNF101
GH19I019402 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.4 -672.6 -672560 5.3 PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF766 CBX5 E2F8 GATAD2A NDUFA13 ENSG00000268030 UPF1 ATP13A1 ENSG00000268938 ELL MAU2 ENSG00000269191 TM6SF2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZNF90 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZNF90 gene promoter:

Genomic Locations for ZNF90 Gene

Genomic Locations for ZNF90 Gene
49,083 bases
Plus strand

Genomic View for ZNF90 Gene

Genes around ZNF90 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZNF90 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZNF90 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZNF90 Gene

Proteins for ZNF90 Gene

  • Protein details for ZNF90 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger protein 90
    Protein Accession:
    Secondary Accessions:
    • B9EH87

    Protein attributes for ZNF90 Gene

    601 amino acids
    Molecular mass:
    69058 Da
    Quaternary structure:
    No Data Available

neXtProt entry for ZNF90 Gene

Post-translational modifications for ZNF90 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ZNF90 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ZNF90 Gene

Domains & Families for ZNF90 Gene

Gene Families for ZNF90 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for ZNF90 Gene

Suggested Antigen Peptide Sequences for ZNF90 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the krueppel C2H2-type zinc-finger protein family.
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with ZNF90: view

Function for ZNF90 Gene

Molecular function for ZNF90 Gene

GENATLAS Biochemistry:
zinc finger protein 90 (HTF9),KRAB subfamily
UniProtKB/Swiss-Prot Function:
May be involved in transcriptional regulation.

Phenotypes From GWAS Catalog for ZNF90 Gene

Gene Ontology (GO) - Molecular Function for ZNF90 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity NAS 2023909
GO:0008270 zinc ion binding NAS 2023909
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZNF90: view
genes like me logo Genes that share phenotypes with ZNF90: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZNF90 Gene

Localization for ZNF90 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZNF90 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ZNF90 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZNF90 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with ZNF90: view

Pathways & Interactions for ZNF90 Gene

SuperPathways for ZNF90 Gene

No Data Available

Interacting Proteins for ZNF90 Gene

Gene Ontology (GO) - Biological Process for ZNF90 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with ZNF90: view

No data available for Pathways by source and SIGNOR curated interactions for ZNF90 Gene

Drugs & Compounds for ZNF90 Gene

No Compound Related Data Available

Transcripts for ZNF90 Gene

mRNA/cDNA for ZNF90 Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(6) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for ZNF90 Gene

Zinc finger protein 90:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZNF90 Gene

No ASD Table

Relevant External Links for ZNF90 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZNF90 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZNF90 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for ZNF90 Gene

NURSA nuclear receptor signaling pathways regulating expression of ZNF90 Gene:


SOURCE GeneReport for Unigene cluster for ZNF90 Gene:


Evidence on tissue expression from TISSUES for ZNF90 Gene

  • Nervous system(3.1)
genes like me logo Genes that share expression patterns with ZNF90: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZNF90 Gene

Orthologs for ZNF90 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZNF90 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZNF90 33 34
  • 99.22 (n)
(Bos Taurus)
Mammalia -- 34
  • 53 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 47 (a)
-- 34
  • 41 (a)
(Canis familiaris)
Mammalia -- 34
  • 38 (a)
(Mus musculus)
Mammalia Zfp386 34
  • 33 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 54 (a)
-- 34
  • 47 (a)
-- 34
  • 39 (a)
-- 34
  • 39 (a)
-- 34
  • 36 (a)
-- 34
  • 35 (a)
-- 34
  • 35 (a)
-- 34
  • 30 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG4046 35
  • 82 (a)
(Caenorhabditis elegans)
Secernentea rps-16 35
  • 72 (a)
Species where no ortholog for ZNF90 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for ZNF90 Gene

Gene Tree for ZNF90 (if available)
Gene Tree for ZNF90 (if available)

Paralogs for ZNF90 Gene

(510) SIMAP similar genes for ZNF90 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with ZNF90: view

Variants for ZNF90 Gene

Sequence variations from dbSNP and Humsavar for ZNF90 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000094274 -- 20,126,041(+) T/C genic_downstream_transcript_variant, non_coding_transcript_variant
rs1000170067 -- 20,115,935(+) G/A intron_variant
rs1000177202 -- 20,091,977(+) T/G intron_variant
rs1000247839 -- 20,096,367(+) C/G intron_variant
rs1000334959 -- 20,087,889(+) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ZNF90 Gene

Variant ID Type Subtype PubMed ID
dgv3456n100 CNV gain 25217958
dgv3457n100 CNV gain 25217958
dgv509e201 CNV deletion 23290073
dgv6303n54 CNV loss 21841781
dgv630e199 CNV deletion 23128226
esv2718296 CNV deletion 23290073
esv2718298 CNV deletion 23290073
esv2718300 CNV deletion 23290073
esv2758748 CNV gain 17122850
esv34357 CNV gain 17911159
esv3643866 CNV loss 21293372
esv3643868 CNV loss 21293372
nsv1057107 CNV gain 25217958
nsv1059188 CNV loss 25217958
nsv1061846 CNV loss 25217958
nsv519535 CNV gain 19592680
nsv578804 CNV gain 21841781
nsv578805 CNV gain 21841781
nsv817820 CNV gain 17921354
nsv963020 CNV duplication 23825009

Variation tolerance for ZNF90 Gene

Residual Variation Intolerance Score: 80.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.11; 80.56% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZNF90 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZNF90 Gene

Disorders for ZNF90 Gene

Additional Disease Information for ZNF90

No disorders were found for ZNF90 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZNF90 Gene

Publications for ZNF90 Gene

  1. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. (PMID: 15146197) Brandenberger R … Stanton LW (Nature biotechnology 2004) 3 4 58
  2. Clustered organization of homologous KRAB zinc-finger genes with enhanced expression in human T lymphoid cells. (PMID: 8467795) Bellefroid EJ … Szpirer C (The EMBO journal 1993) 2 3 58
  3. The evolutionarily conserved Krüppel-associated box domain defines a subfamily of eukaryotic multifingered proteins. (PMID: 2023909) Bellefroid EJ … Martial JA (Proceedings of the National Academy of Sciences of the United States of America 1991) 3 4 58
  4. Toward a confocal subcellular atlas of the human proteome. (PMID: 18029348) Barbe L … Andersson-Svahn H (Molecular & cellular proteomics : MCP 2008) 3 58
  5. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 4 58

Products for ZNF90 Gene

Sources for ZNF90 Gene

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