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ZNF90 Gene

protein-coding   GIFtS: 40
GCID: GC19P020188

Zinc Finger Protein 90

(Previous name: zinc finger protein 90 (HTF9))
  Search for ZNF90
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Zinc Finger Protein 901 2
Zinc Finger Protein HTF92 3
Zinc Finger Protein 90 (HTF9)1
HTF92

External Ids:    HGNC: 131651   Entrez Gene: 76432   Ensembl: ENSG000002139887   OMIM: 6039735   UniProtKB: Q039383   

Export aliases for ZNF90 gene to outside databases

Previous GC identifers: GC19P020725 GC19P020580 GC19P020034 GC19P020073 GC19P020049 GC19P020076 GC19U900566 GC19P019977


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for ZNF90 Gene:
ZNF90 (zinc finger protein 90) is a protein-coding gene. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity. An important paralog of this gene is ZNF85.

UniProtKB/Swiss-Prot: ZNF90_HUMAN, Q03938
Function: May be involved in transcriptional regulation




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000019.10  NC_018930.2  NT_011295.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the ZNF90 gene promoter:
         AML1a   FOXO3   Evi-1   FOXO3b   COMP1   Cart-1   FOXO1a   FOXO3a   FOXO1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for ZNF90

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZNF90


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19p12   Ensembl cytogenetic band:  19p12   HGNC cytogenetic band: 19p12

ZNF90 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZNF90 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P020188:  view genomic region     (about GC identifiers)

Start:
20,188,803 bp from pter      End:
20,237,885 bp from pter
Size:
49,083 bases      Orientation:
plus strand

1 alternative location:
Chr19+,NW_003571053 21,491-38,421     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: ZNF90_HUMAN, Q03938 (See protein sequence)
Recommended Name: Zinc finger protein 90  
Size: 601 amino acids; 69058 Da
Developmental stage: Expressed early during embryonic development
Secondary accessions: B9EH87

Explore the universe of human proteins at neXtProt for ZNF90: NX_Q03938

Explore proteomics data for ZNF90 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys208, Lys339, Lys342
  • Modification sites at PhosphoSitePlus

  • See ZNF90 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_009069.1  
    ENSEMBL proteins: 
     ENSP00000420111   ENSP00000418166   ENSP00000410466  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ZNF: Zinc fingers, C2H2-type

    4 InterPro protein domains:
     IPR001909 Krueppel-associated_box
     IPR015880 Znf_C2H2-like
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2

    Graphical View of Domain Structure for InterPro Entry Q03938

    ProtoNet protein and cluster: Q03938

    1 Blocks protein domain: IPB001909 KRAB box

    UniProtKB/Swiss-Prot: ZNF90_HUMAN, Q03938
    Similarity: Belongs to the krueppel C2H2-type zinc-finger protein family
    Similarity: Contains 15 C2H2-type zinc fingers
    Similarity: Contains 1 KRAB domain


    ZNF90 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ZNF90_HUMAN, Q03938
    Function: May be involved in transcriptional regulation

         Genatlas biochemistry entry for ZNF90:
    zinc finger protein 90 (HTF9),KRAB subfamily

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity NAS2023909
    GO:0008270zinc ion binding NAS2023909
    GO:0046872metal ion binding ----
         
    ZNF90 for ontologies           About GeneDecksing


    Animal Models:
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    ZNF90_HUMAN, Q03938: Nucleus (Probable)

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus IEA--
    GO:0005794Golgi apparatus ----

    ZNF90 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for ZNF90
    Interactions:

        Search GeneGlobe Interaction Network for ZNF90

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated ----

    ZNF90 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for ZNF90



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for ZNF90 gene: 
    NM_007138.1  

    Unigene Cluster for ZNF90:

    Zinc finger protein 90
    Hs.55304  [show with all ESTs]
    Unigene Representative Sequence: NM_007138
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000469078 ENST00000474284(uc021url.1) ENST00000473524 ENST00000418063(uc002nor.2)
    ENST00000492328 ENST00000484032
    miRNA
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    1 qRT-PCR Assays for microRNA that regulate ZNF90:
    hsa-miR-188-3p
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for ZNF90
    Predesigned siRNA for gene silencing in human, mouse, rat ZNF90
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    Pre-validated RT2 qPCR Primer Assay in human, mouse / rat ZNF90
      QuantiTect SYBR Green Assays in human, mouse, rat ZNF90
      QuantiFast Probe-based Assays in human, mouse, rat ZNF90

    Additional mRNA sequence: 

    AK298173.1 BC137211.1 M61870.1 

    18 DOTS entries:

    DT.99995515  DT.450891  DT.91722009  DT.91744579  DT.99972817  DT.91640964  DT.100020145  DT.100804400 
    DT.121457166  DT.40316414  DT.433029  DT.439064  DT.450351  DT.91779566  DT.91917593  DT.95100464 
    DT.95150319  DT.97858455 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    ZNF90 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATGAAAATAT
    ZNF90 Expression
    About this image

    ZNF90 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZNF90 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.55304
        Custom PCR Arrays for ZNF90
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZNF90

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for ZNF90 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 8)
    Uncharacterized protein
    (see all 8)
    54(a)
    47(a)
    (see all 8)
    many ↔ many
    many ↔ many
    (see all 8)
    AAWZ02037240(11818-13836)
    GL343434.1(292314-296903)
            Species with no ortholog for ZNF90

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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ZNF90 gene
    ZNF852  ZNF4862  ZNF1952  ZNF922  ZNF1002  ZNF7322  ZNF6752  ZNF1382  
    ZNF5062  ZNF662  ZNF2732  ZNF6952  ZNF6262  ZNF6802  ZNF4792  ZNF2532  
    ZNF932  ZNF6822  ZNF4922  ZNF6762  ZNF6812  ZNF1412  ZNF7362  ZNF6792  
    ZNF2572  ZNF2542  ZNF7372  ZNF724P2  ZNF982  ZNF7162  ZNF7142  ZNF4292  
    ZNF5192  ZNF4302  ZNF7302  ZNF7082  ZNF1172  ZNF4312  ZNF7262  ZNF7282  
    Selected SIMAP similar genes for ZNF90 using alignment to 3 protein entries:     ZNF90_HUMAN (see all proteins) (see all similar genes):
    ZNF506    MGC12518    ZNF93    ZNF724P    ZNF257    ZNF98
    ZNF66    ZNF273    ZNF737    ZNF100    ZNF43    ZNF730
    ZNF675    ZNF430    ZNF208    ZNF486    ZNF726    ZNF429

    ZNF90 for paralogs           About GeneDecksing


    Selected Pseudogenes.org Pseudogenes for ZNF90 (see all 6)
    PGOHUM00000259306 PGOHUM00000259311 PGOHUM00000262381 PGOHUM00000262383 PGOHUM00000234564


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for ZNF90 (see all 1122)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs104211311,2
    C,F--20186901(+) gagctG/Ctcacg 1 -- us2k16Minor allele frequency- C:0.33NA WA CSA EA 246
    rs104211321,2
    C,F--20186906(+) gtcacG/Aaagct 1 -- us2k15Minor allele frequency- A:0.09NA WA EA 244
    rs747533331,2
    C,F--20186917(+) TTGGCG/ACAGTC 1 -- us2k11Minor allele frequency- A:0.04EA 120
    rs1388417261,2
    --20186959(+) TGGCAC/TGAGGC 1 -- us2k10--------
    rs1162769231,2
    F--20186985(+) CTTCGC/TGACTG 1 -- us2k11Minor allele frequency- T:0.05WA 118
    rs578857381,2
    C--20187046(+) TTCAAG/TAACGA 1 -- us2k13Minor allele frequency- T:0.24CSA WA EA 240
    rs1822922131,2
    --20187058(+) TGTATA/GGGAAT 1 -- us2k10--------
    rs1869089861,2
    --20187078(+) TACAGA/TTTTCT 1 -- us2k10--------
    rs1926609891,2
    C--20187114(+) CTAGGC/GGCTCA 1 -- us2k10--------
    rs1849490351,2
    --20187119(+) GGCTCA/CCACAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ZNF90 (20188803 - 20237885 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for ZNF90 (see all 18):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2718298CNV Deletion23290073
    dgv550e201CNV Deletion23290073
    esv2718300CNV Deletion23290073
    esv2718296CNV Deletion23290073
    dgv630e199CNV Deletion23128226
    nsv911327CNV Loss21882294
    dgv3794n71CNV Loss21882294
    dgv3792n71CNV Gain21882294
    nsv911322CNV Gain21882294
    nsv911321CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ZNF90
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 603973    OMIM disorders: --


    ZNF90 for disorders           About GeneDecksing


    Export disorders for ZNF90 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for ZNF90 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with ZNF90)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. (PubMed id 15146197)1, 2 Brandenberger R.... Stanton L.W. (Nat. Biotechnol. 2004)
    2. Clustered organization of homologous KRAB zinc-finger genes with enhanced expression in human T lymphoid cells. (PubMed id 8467795)1, 3 Bellefroid E.J.... Martial J.A. (EMBO J. 1993)
    3. The evolutionarily conserved Kruppel-associated box domain defines a subfamily of eukaryotic multifingered proteins. (PubMed id 2023909)1, 2 Bellefroid E.J....Martial J.A. (Proc. Natl. Acad. Sci. U.S.A. 1991)
    4. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    5. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    7. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (Nature 2004)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    9. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (Science 2001)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 7643 HGNC: 13165 Ensembl:ENSG00000213988 euGenes: HUgn7643 ECgene: ZNF90
    H-InvDB: ZNF90

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for ZNF90 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for ZNF90 gene:
    Search GeneIP for patents involving ZNF90

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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