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ZNF558 zinc finger protein 558 [ Homo sapiens (human) ]

Gene ID: 148156, updated on 11-Apr-2024

Summary

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Official Symbol
ZNF558provided by HGNC
Official Full Name
zinc finger protein 558provided by HGNC
Primary source
HGNC:HGNC:26422
See related
Ensembl:ENSG00000167785 AllianceGenome:HGNC:26422
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
Ubiquitous expression in endometrium (RPKM 6.2), thyroid (RPKM 6.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
19p13.2
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (8806170..8838144, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (8917114..8949099, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (8916846..8942980, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene actin like 9 Neighboring gene ribosomal protein L23a pseudogene 78 Neighboring gene olfactory receptor family 2 subfamily Z member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10035 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10036 Neighboring gene methyl-CpG binding domain protein 3 like 1 Neighboring gene mucin 16, cell surface associated Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:9070485-9071684 Neighboring gene MPRA-validated peak3341 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:9150106-9151305 Neighboring gene bolA family member 3 pseudogene 2 Neighboring gene tRNA-Gln (anticodon TTG) 8-1

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 cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development. Johansson PA, et al. Cell Stem Cell, 2022 Jan 6. PMID 34624206
  2. Interactome mapping suggests new mechanistic details underlying Alzheimer's disease. Soler-López M, et al. Genome Res, 2011 Mar. PMID 21163940, Free PMC Article
  3. A protein interaction framework for human mRNA degradation. Lehner B, et al. Genome Res, 2004 Jul. PMID 15231747, Free PMC Article
  4. Cullin 3 Exon 9 Deletion in Familial Hyperkalemic Hypertension Impairs Cullin3-Ring-E3 Ligase (CRL3) Dynamic Regulation and Cycling. Kouranti I, et al. Int J Mol Sci, 2022 May 5. PMID 35563538, Free PMC Article
  5. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development.
    Title: A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development.
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

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ30932

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
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
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 cellular_component ND
No biological Data available
more info
  
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 558

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_001304350.2 → NP_001291279.1  zinc finger protein 558 isoform 2

    See identical proteins and their annotated locations for NP_001291279.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' structure, lacks a portion of the 5' coding region, and initiates translation from a downstream start site compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC008734, AC012616, AK301664, BC064356, BM728437, DB547630
    UniProtKB/Swiss-Prot
    Q96NG5
    Conserved Domains (3) summary
    COG5048
    Location:91 → 327
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:223 → 243
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cl02581
    Location:1 → 29
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

  2. NM_144693.3 → NP_653294.1  zinc finger protein 558 isoform 1

    See identical proteins and their annotated locations for NP_653294.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC008734, AC012616, AK291265, AK307200, BC064356, DB478966, DB547630
    Consensus CDS
    CCDS12208.1
    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5
    Related
    ENSP00000471277.1, ENST00000601372.6
    Conserved Domains (3) summary
    smart00349
    Location:43 → 100
    KRAB; krueppel associated box
    COG5048
    Location:162 → 398
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:294 → 314
    ZF_C2H2; C2H2 Zn finger [structural motif]

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
    8806170..8838144 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024451393.2 → XP_024307161.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5
    Related
    ENSP00000301475.1, ENST00000301475.1
    Conserved Domains (3) summary
    smart00349
    Location:43 → 100
    KRAB; krueppel associated box
    COG5048
    Location:162 → 398
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:294 → 314
    ZF_C2H2; C2H2 Zn finger [structural motif]

  2. XM_024451391.2 → XP_024307159.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5
    Conserved Domains (3) summary
    smart00349
    Location:43 → 100
    KRAB; krueppel associated box
    COG5048
    Location:162 → 398
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:294 → 314
    ZF_C2H2; C2H2 Zn finger [structural motif]

  3. XM_024451389.2 → XP_024307157.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5
    Conserved Domains (3) summary
    smart00349
    Location:43 → 100
    KRAB; krueppel associated box
    COG5048
    Location:162 → 398
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:294 → 314
    ZF_C2H2; C2H2 Zn finger [structural motif]

  4. XM_024451387.2 → XP_024307155.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5
    Conserved Domains (3) summary
    smart00349
    Location:43 → 100
    KRAB; krueppel associated box
    COG5048
    Location:162 → 398
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:294 → 314
    ZF_C2H2; C2H2 Zn finger [structural motif]

  5. XM_024451395.2 → XP_024307163.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5
    Conserved Domains (3) summary
    smart00349
    Location:43 → 100
    KRAB; krueppel associated box
    COG5048
    Location:162 → 398
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:294 → 314
    ZF_C2H2; C2H2 Zn finger [structural motif]

  6. XM_024451394.2 → XP_024307162.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5
    Conserved Domains (3) summary
    smart00349
    Location:43 → 100
    KRAB; krueppel associated box
    COG5048
    Location:162 → 398
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:294 → 314
    ZF_C2H2; C2H2 Zn finger [structural motif]

  7. XM_024451386.2 → XP_024307154.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5
    Conserved Domains (3) summary
    smart00349
    Location:43 → 100
    KRAB; krueppel associated box
    COG5048
    Location:162 → 398
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:294 → 314
    ZF_C2H2; C2H2 Zn finger [structural motif]

  8. XM_047438268.1 → XP_047294224.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  9. XM_024451390.2 → XP_024307158.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5
    Conserved Domains (3) summary
    smart00349
    Location:43 → 100
    KRAB; krueppel associated box
    COG5048
    Location:162 → 398
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:294 → 314
    ZF_C2H2; C2H2 Zn finger [structural motif]

  10. XM_024451388.2 → XP_024307156.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5
    Conserved Domains (3) summary
    smart00349
    Location:43 → 100
    KRAB; krueppel associated box
    COG5048
    Location:162 → 398
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:294 → 314
    ZF_C2H2; C2H2 Zn finger [structural motif]

  11. XM_047438269.1 → XP_047294225.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  12. XM_047438270.1 → XP_047294226.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  13. XM_047438271.1 → XP_047294227.1  zinc finger protein 558 isoform X2

  14. XM_011527703.3 → XP_011526005.1  zinc finger protein 558 isoform X2

    See identical proteins and their annotated locations for XP_011526005.1

    UniProtKB/Swiss-Prot
    Q96NG5
    Conserved Domains (3) summary
    COG5048
    Location:91 → 327
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:223 → 243
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cl02581
    Location:1 → 29
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791807.1 Reference GRCh38.p14 PATCHES

    Range
    41113..73087 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333245.1 → XP_054189220.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  2. XM_054333234.1 → XP_054189209.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  3. XM_054333241.1 → XP_054189216.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  4. XM_054333242.1 → XP_054189217.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  5. XM_054333243.1 → XP_054189218.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  6. XM_054333244.1 → XP_054189219.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  7. XM_054333236.1 → XP_054189211.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  8. XM_054333238.1 → XP_054189213.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  9. XM_054333237.1 → XP_054189212.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  10. XM_054333240.1 → XP_054189215.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  11. XM_054333239.1 → XP_054189214.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  12. XM_054333235.1 → XP_054189210.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  13. XM_054333247.1 → XP_054189222.1  zinc finger protein 558 isoform X2

  14. XM_054333246.1 → XP_054189221.1  zinc finger protein 558 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    8917114..8949099 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319997.1 → XP_054175972.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  2. XM_054319986.1 → XP_054175961.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  3. XM_054319993.1 → XP_054175968.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  4. XM_054319994.1 → XP_054175969.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  5. XM_054319995.1 → XP_054175970.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  6. XM_054319996.1 → XP_054175971.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  7. XM_054319988.1 → XP_054175963.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  8. XM_054319990.1 → XP_054175965.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  9. XM_054319989.1 → XP_054175964.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  10. XM_054319992.1 → XP_054175967.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  11. XM_054319991.1 → XP_054175966.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  12. XM_054319987.1 → XP_054175962.1  zinc finger protein 558 isoform X1

    UniProtKB/Swiss-Prot
    A8K5F0, B7Z798, Q96NG5

  13. XM_054319999.1 → XP_054175974.1  zinc finger protein 558 isoform X2

  14. XM_054319998.1 → XP_054175973.1  zinc finger protein 558 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96NG5.1 GenPept UniProtKB/Swiss-Prot:Q96NG5

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