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

    Gene ID: 148156, updated on 10-Dec-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 factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in endometrium (RPKM 6.2), thyroid (RPKM 6.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZNF558 in Genome Data Viewer
    Location:
    19p13.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (8806170..8838144, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (8917114..8949099, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. Acetylation-Mimic Mutation of TRIM28-Lys304 to Gln Attenuates the Interaction with KRAB-Zinc-Finger Proteins and Affects Gene Expression in Leukemic K562 Cells. Chang YJ, et al. Int J Mol Sci, 2023 Jun 6. PMID 37372979, Free PMC Article
    4. A protein interaction framework for human mRNA degradation. Lehner B, et al. Genome Res, 2004 Jul. PMID 15231747, Free PMC Article
    5. Chr21 protein-protein interactions: enrichment in proteins involved in intellectual disability, autism, and late-onset Alzheimer's disease. Viard J, et al. Life Sci Alliance, 2022 Aug 1. PMID 35914814, Free PMC Article

    See all (16) 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)

    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 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 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_2024_08

    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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