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

Gene ID: 80032, updated on 4-Dec-2022

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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See ZNF556 in Genome Data Viewer
Location:
19p13.3
Exon count:
4
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2867335..2883445)
110 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 zinc finger protein 554 Neighboring gene zinc finger protein 555 Neighboring gene 60S ribosomal protein L35a-like Neighboring gene zinc finger protein 57 pseudogene 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. 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
  2. A whole genome screen for HIV restriction factors. Liu L, et al. Retrovirology, 2011 Nov 14. PMID 22082156, Free PMC Article
  3. An atlas of combinatorial transcriptional regulation in mouse and man. Ravasi T, et al. Cell, 2010 Mar 5. PMID 20211142, Free PMC Article
  4. Ubiquitin-mediated proteolysis of HuR by heat shock. Abdelmohsen K, et al. EMBO J, 2009 May 6. PMID 19322201, Free PMC Article
  5. 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

See all (12) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

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
 PubMed 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
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/Swiss-Prot
    Q9HAH1
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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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