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    ZFP90 ZFP90 zinc finger protein [ Homo sapiens (human) ]

    Gene ID: 146198, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ZFP90provided by HGNC
    Official Full Name
    ZFP90 zinc finger proteinprovided by HGNC
    Primary source
    HGNC:HGNC:23329
    See related
    Ensembl:ENSG00000184939 MIM:609451; AllianceGenome:HGNC:23329
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    FIK; NK10; ZNF756; zfp-90
    Summary
    This gene encodes a member of the zinc finger protein family that modulates gene expression. The encoded protein derepresses the transcription of certain fetal cardiac genes and may contribute to the genetic reprogramming that occurs during the development of heart failure. Genome wide association studies have identified this gene among ulcerative colitis risk loci. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Mar 2015]
    Expression
    Ubiquitous expression in ovary (RPKM 6.9), brain (RPKM 6.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZFP90 in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (68533479..68576506)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (74323667..74372339)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68573194..68609975)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein L35a pseudogene 33 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68541928-68542428 Neighboring gene uncharacterized LOC105371321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11023 Neighboring gene RNA, U4 small nuclear 36, pseudogene Neighboring gene small nucleolar RNA U109 Neighboring gene uncharacterized LOC124903809

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Assessing the Function of the ZFP90 Variant rs1170426 in SLE and the Association Between SLE Drug Target and Susceptibility Genes. Zhu T, et al. Front Immunol, 2021. PMID 33796098, Free PMC Article
    2. Spastic paraplegia, optic atrophy, and neuropathy is linked to chromosome 11q13. Macedo-Souza LI, et al. Ann Neurol, 2005 May. PMID 15852396
    3. A 16q22.1 variant confers susceptibility to colorectal cancer as a distal regulator of ZFP90. Yu CY, et al. Oncogene, 2020 Feb. PMID 31641208, Free PMC Article
    4. Cutting Edge: a novel, human-specific interacting protein couples FOXP3 to a chromatin-remodeling complex that contains KAP1/TRIM28. Huang C, et al. J Immunol, 2013 May 1. PMID 23543754, Free PMC Article
    5. Zinc-finger protein 90 negatively regulates neuron-restrictive silencer factor-mediated transcriptional repression of fetal cardiac genes. Hata L, et al. J Mol Cell Cardiol, 2011 Jun. PMID 21284946

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Assessing the Function of the ZFP90 Variant rs1170426 in SLE and the Association Between SLE Drug Target and Susceptibility Genes.
      Title: Assessing the Function of the ZFP90 Variant rs1170426 in SLE and the Association Between SLE Drug Target and Susceptibility Genes.
    2. A 16q22.1 variant confers susceptibility to colorectal cancer as a distal regulator of ZFP90.
      Title: A 16q22.1 variant confers susceptibility to colorectal cancer as a distal regulator of ZFP90.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.
    EBI GWAS Catalog
    Genome-wide pharmacogenomic study of neurocognition as an indicator of antipsychotic treatment response in schizophrenia.
    EBI GWAS Catalog
    Genomewide association study for determinants of HIV-1 acquisition and viral set point in HIV-1 serodiscordant couples with quantified virus exposure.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 90 homolog
    Names
    FOXP3-interacting KRAB domain-containing protein
    zinc finger protein 476
    zinc finger protein 756

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001305203.2 → NP_001292132.1  zinc finger protein 90 homolog isoform 1

      See identical proteins and their annotated locations for NP_001292132.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein (isoform 1).
      Source sequence(s)
      AC009162, AC126773
      Consensus CDS
      CCDS42183.1
      UniProtKB/Swiss-Prot
      B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6
      Related
      ENSP00000454418.2, ENST00000563169.7
      Conserved Domains (3) summary
      smart00349
      Location:14 → 74
      KRAB; krueppel associated box
      COG5048
      Location:336 → 632
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:555 → 575
      ZF_C2H2; C2H2 Zn finger [structural motif]

    2. NM_001305204.2 → NP_001292133.1  zinc finger protein 90 homolog isoform 2

      See identical proteins and their annotated locations for NP_001292133.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate 3' terminal exon, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC009162, AC126773, AW135652
      Consensus CDS
      CCDS76892.1
      UniProtKB/TrEMBL
      I3L0X7
      Related
      ENSP00000480309.1, ENST00000611381.4
      Conserved Domains (1) summary
      smart00349
      Location:14 → 74
      KRAB; krueppel associated box

    3. NM_001305206.2 → NP_001292135.1  zinc finger protein 90 homolog isoform 3

      See identical proteins and their annotated locations for NP_001292135.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate splice site in the 3' coding region, compared to variant 1. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 1. Both variants 4 and 5 encode the same protein (isoform 3).
      Source sequence(s)
      AC009162, AC126773
      Consensus CDS
      CCDS82003.1
      UniProtKB/TrEMBL
      H3BVC6, J3QKQ8
      Conserved Domains (1) summary
      smart00349
      Location:14 → 74
      KRAB; krueppel associated box

    4. NM_001305207.2 → NP_001292136.1  zinc finger protein 90 homolog isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and uses an alternate splice site in the 3' coding region, compared to variant 1. It encodes isoform 4 which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC009162, AC126773
      UniProtKB/TrEMBL
      H3BVC6
      Conserved Domains (1) summary
      smart00349
      Location:14 → 74
      KRAB; krueppel associated box

    5. NM_001305208.2 → NP_001292137.1  zinc finger protein 90 homolog isoform 3

      See identical proteins and their annotated locations for NP_001292137.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in the 3' coding region, compared to variant 1. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 1. Both variants 4 and 5 encode the same protein (isoform 3).
      Source sequence(s)
      AC009162, AC126773
      Consensus CDS
      CCDS82003.1
      UniProtKB/TrEMBL
      H3BVC6, J3QKQ8
      Related
      ENSP00000463193.1, ENST00000564323.5
      Conserved Domains (1) summary
      smart00349
      Location:14 → 74
      KRAB; krueppel associated box

    6. NM_133458.4 → NP_597715.2  zinc finger protein 90 homolog isoform 1

      See identical proteins and their annotated locations for NP_597715.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest protein. Both variants 1 and 2 encode the same protein (isoform 1).
      Source sequence(s)
      AC009162, AC126773
      Consensus CDS
      CCDS42183.1
      UniProtKB/Swiss-Prot
      B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6
      Related
      ENSP00000460547.1, ENST00000570495.5
      Conserved Domains (3) summary
      smart00349
      Location:14 → 74
      KRAB; krueppel associated box
      COG5048
      Location:336 → 632
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:555 → 575
      ZF_C2H2; C2H2 Zn finger [structural motif]

    RNA

    1. NR_130976.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) uses an alternate splice sites in the 5'-most exon and an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC009162, AC126773
      Related
      ENST00000564558.5

    2. NR_130977.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) uses an alternate splice sites in the 5'-most exon and an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC009162, AC126773

    3. NR_130978.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) uses an alternate splice sites in the 5'-most exon and an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC009162, AC126773

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      68533479..68576506
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017022952.3 → XP_016878441.1  zinc finger protein 90 homolog isoform X1

    2. XM_024450159.2 → XP_024305927.1  zinc finger protein 90 homolog isoform X2

      UniProtKB/Swiss-Prot
      B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6
      Related
      ENSP00000381304.2, ENST00000398253.6
      Conserved Domains (3) summary
      smart00349
      Location:14 → 74
      KRAB; krueppel associated box
      COG5048
      Location:336 → 632
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:555 → 575
      ZF_C2H2; C2H2 Zn finger [structural motif]

    3. XM_047433640.1 → XP_047289596.1  zinc finger protein 90 homolog isoform X3

      UniProtKB/TrEMBL
      I3L0X7

    4. XM_047433641.1 → XP_047289597.1  zinc finger protein 90 homolog isoform X3

      UniProtKB/TrEMBL
      I3L0X7

    5. XM_047433639.1 → XP_047289595.1  zinc finger protein 90 homolog isoform X3

      UniProtKB/TrEMBL
      I3L0X7

    6. XM_047433642.1 → XP_047289598.1  zinc finger protein 90 homolog isoform X4

      UniProtKB/TrEMBL
      H3BVC6, J3QKQ8

    7. XM_005255804.3 → XP_005255861.1  zinc finger protein 90 homolog isoform X2

      See identical proteins and their annotated locations for XP_005255861.1

      UniProtKB/Swiss-Prot
      B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6
      Conserved Domains (3) summary
      smart00349
      Location:14 → 74
      KRAB; krueppel associated box
      COG5048
      Location:336 → 632
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:555 → 575
      ZF_C2H2; C2H2 Zn finger [structural motif]

    8. XM_047433643.1 → XP_047289599.1  zinc finger protein 90 homolog isoform X5

      UniProtKB/TrEMBL
      H3BVC6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      74323667..74372339
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379640.1 → XP_054235615.1  zinc finger protein 90 homolog isoform X6

    2. XM_054379637.1 → XP_054235612.1  zinc finger protein 90 homolog isoform X1

    3. XM_054379639.1 → XP_054235614.1  zinc finger protein 90 homolog isoform X2

      UniProtKB/Swiss-Prot
      B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6

    4. XM_054379642.1 → XP_054235617.1  zinc finger protein 90 homolog isoform X3

      UniProtKB/TrEMBL
      I3L0X7

    5. XM_054379643.1 → XP_054235618.1  zinc finger protein 90 homolog isoform X3

      UniProtKB/TrEMBL
      I3L0X7

    6. XM_054379641.1 → XP_054235616.1  zinc finger protein 90 homolog isoform X3

      UniProtKB/TrEMBL
      I3L0X7

    7. XM_054379644.1 → XP_054235619.1  zinc finger protein 90 homolog isoform X4

      UniProtKB/TrEMBL
      H3BVC6, J3QKQ8

    8. XM_054379638.1 → XP_054235613.1  zinc finger protein 90 homolog isoform X2

      UniProtKB/Swiss-Prot
      B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6

    9. XM_054379645.1 → XP_054235620.1  zinc finger protein 90 homolog isoform X5

      UniProtKB/TrEMBL
      H3BVC6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TF47.2 GenPept UniProtKB/Swiss-Prot:Q8TF47

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