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

Gene ID: 146198, updated on 7-Jun-2020

Summary

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
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

Genomic context

See ZFP90 in Genome Data Viewer
Location:
16q22.1
Exon count:
8
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (68530249..68576072)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68573192..68609975)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein L35a pseudogene 33 Neighboring gene uncharacterized LOC105371321 Neighboring gene RNA, U4 small nuclear 36, pseudogene Neighboring gene calponin 2 pseudogene Neighboring gene cadherin 3 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 5

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

General protein information

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)

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_001305203.2NP_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
    Q8TF47
    Related
    ENSP00000454418.2, ENST00000563169.7
    Conserved Domains (3) summary
    smart00349
    Location:1474
    KRAB; krueppel associated box
    COG5048
    Location:336632
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:555575
    ZF_C2H2; C2H2 Zn finger [structural motif]
  2. NM_001305204.1NP_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/Swiss-Prot
    Q8TF47
    Related
    ENSP00000480309.1, ENST00000611381.4
    Conserved Domains (1) summary
    smart00349
    Location:1474
    KRAB; krueppel associated box
  3. NM_001305206.2NP_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
    J3QKQ8
    Conserved Domains (2) summary
    smart00349
    Location:1474
    KRAB; krueppel associated box
    pfam01352
    Location:1453
    KRAB; KRAB box
  4. NM_001305207.2NP_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
    Conserved Domains (2) summary
    smart00349
    Location:1474
    KRAB; krueppel associated box
    pfam01352
    Location:1453
    KRAB; KRAB box
  5. NM_001305208.2NP_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
    J3QKQ8
    Related
    ENSP00000463193.1, ENST00000564323.5
    Conserved Domains (2) summary
    smart00349
    Location:1474
    KRAB; krueppel associated box
    pfam01352
    Location:1453
    KRAB; KRAB box
  6. NM_133458.4NP_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
    Q8TF47
    Related
    ENSP00000460547.1, ENST00000570495.5
    Conserved Domains (3) summary
    smart00349
    Location:1474
    KRAB; krueppel associated box
    COG5048
    Location:336632
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:555575
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    68530249..68576072
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (3) summary
    smart00349
    Location:1474
    KRAB; krueppel associated box
    COG5048
    Location:336632
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:555575
    ZF_C2H2; C2H2 Zn finger [structural motif]
  2. XM_017022952.2XP_016878441.1  zinc finger protein 90 homolog isoform X1

  3. XM_005255804.2XP_005255861.1  zinc finger protein 90 homolog isoform X2

    See identical proteins and their annotated locations for XP_005255861.1

    UniProtKB/Swiss-Prot
    Q8TF47
    Conserved Domains (3) summary
    smart00349
    Location:1474
    KRAB; krueppel associated box
    COG5048
    Location:336632
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:555575
    ZF_C2H2; C2H2 Zn finger [structural motif]
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