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    ZNF556 zinc finger protein 556 [ Homo sapiens (human) ]

    Gene ID: 80032, updated on 11-Apr-2024

    Summary

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    Official Symbol
    ZNF556provided by HGNC
    Official Full Name
    zinc finger protein 556provided by HGNC
    Primary source
    HGNC:HGNC:25669
    See related
    Ensembl:ENSG00000172000 AllianceGenome:HGNC:25669
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in ovary (RPKM 2.7), testis (RPKM 0.5) and 4 other tissues See more
    Orthologs
    all
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    Genomic context

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    Location:
    19p13.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2867335..2883445)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2842602..2858723)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (2867333..2883443)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2820277-2820970 Neighboring gene zinc finger protein 554 Neighboring gene MPRA-validated peak3238 silencer Neighboring gene MPRA-validated peak3239 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9814 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9815 Neighboring gene zinc finger protein 555 Neighboring gene ribosomal protein L35a pseudogene 38 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2887583-2887760 Neighboring gene zinc finger protein 57 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9816 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:2900543-2901114 Neighboring gene zinc finger protein 57

    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. A whole genome screen for HIV restriction factors. Liu L, et al. Retrovirology, 2011 Nov 14. PMID 22082156, Free PMC Article
    2. An atlas of combinatorial transcriptional regulation in mouse and man. Ravasi T, et al. Cell, 2010 Mar 5. PMID 20211142, Free PMC Article
    3. Ubiquitin-mediated proteolysis of HuR by heat shock. Abdelmohsen K, et al. EMBO J, 2009 May 6. PMID 19322201, Free PMC Article
    4. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Maruyama K, et al. Gene, 1994 Jan 28. PMID 8125298
    5. TRABID targets DDB2 for deubiquitination to promote proliferation of hepatocellular carcinoma cells. Chen Y, et al. Biochem Biophys Res Commun, 2022 Oct 15. PMID 35944360

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of zinc finger protein 556 (ZNF556) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11637

    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 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
    		  
    Process Evidence Code Pubs
    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 556

    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_001300843.2 → NP_001287772.1  zinc finger protein 556 isoform 2

      See identical proteins and their annotated locations for NP_001287772.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter by an amino-acid, compared to isoform 1.
      Source sequence(s)
      AK225297, BC009374
      Consensus CDS
      CCDS74254.1
      UniProtKB/TrEMBL
      A0A0C4DGQ3
      Related
      ENSP00000467366.1, ENST00000586426.5
      Conserved Domains (3) summary
      COG5048
      Location:145 → 293
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:148 → 168
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:14 → 44
      KRAB; KRAB box

    2. NM_024967.3 → NP_079243.1  zinc finger protein 556 isoform 1

      See identical proteins and their annotated locations for NP_079243.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC006130, AK021699, BC009374
      Consensus CDS
      CCDS12097.1
      UniProtKB/Swiss-Prot
      Q96GM3, Q9HAH1
      Related
      ENSP00000302603.2, ENST00000307635.3
      Conserved Domains (5) summary
      COG5048
      Location:146 → 294
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:149 → 169
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:175 → 197
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:14 → 43
      KRAB; KRAB box
      pfam13465
      Location:217 → 242
      zf-H2C2_2; Zinc-finger double domain

    RNA

    1. NR_145838.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC006130

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      2867335..2883445
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      2842602..2858723
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HAH1.1 GenPept UniProtKB/Swiss-Prot:Q9HAH1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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