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    ZNF542P zinc finger protein 542, pseudogene [ Homo sapiens (human) ]

    Gene ID: 147947, updated on 10-Oct-2023

    Summary

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    Official Symbol
    ZNF542Pprovided by HGNC
    Official Full Name
    zinc finger protein 542, pseudogeneprovided by HGNC
    Primary source
    HGNC:HGNC:25393
    See related
    Ensembl:ENSG00000290720 AllianceGenome:HGNC:25393
    Gene type
    pseudo
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ZNF542
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-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, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 6.2), testis (RPKM 5.6) and 25 other tissues See more
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    Genomic context

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    See ZNF542P in Genome Data Viewer
    Location:
    19q13.43
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (56368099..56379828)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (59462491..59474231)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (56879468..56891197)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger and SCAN domain containing 5A Neighboring gene ZSCAN5A antisense RNA 1 Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 1 pseudogene Neighboring gene vomeronasal 2 receptor 18 pseudogene Neighboring gene Sharpr-MPRA regulatory region 13801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15118 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:56888366-56889565 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:56895030-56896229 Neighboring gene SLC25A36 pseudogene 1 Neighboring gene zinc finger protein 582 Neighboring gene ZNF582 divergent transcript

    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. ZNF542P is a pseudogene associated with LDL response to simvastatin treatment. Kim K, et al. Sci Rep, 2018 Aug 20. PMID 30127457, Free PMC Article
    2. Targeted bisulfite sequencing identified a panel of DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC). Pu W, et al. Clin Epigenetics, 2017. PMID 29270239, Free PMC Article
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A role for ZNF542P in LDLC response to simvastatin.
      Title: ZNF542P is a pseudogene associated with LDL response to simvastatin treatment.
    2. Integration analysis of esophageal squamous cell carcinoma (ESCC) identified five hyper-methylated CpG sites in STK3, ZNF418 and ZNF542 that can be used for effective methylation-based testing for ESCC diagnosis.
      Title: Targeted bisulfite sequencing identified a panel of DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC).
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    General gene information

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    Markers

    Other Names

    • zinc finger protein pseudogene

    Clone Names

    • DKFZp686B2197, DKFZp686I1219

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    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.

    RNA

    1. NR_003127.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has an alternate first exon, includes an additional internal exon in the 5' region, and uses an alternate splice site in an internal exon in the 3' region, compared to variant 1.
      Source sequence(s)
      AC006116, BC089419, BX640680, DB051263
      Related
      ENST00000467807.5

    2. NR_024055.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) has an alternate first exon, includes an additional internal exon in the 5' region, and lacks an internal exon in the 3' region, compared to variant 1.
      Source sequence(s)
      AC006116, DA095148

    3. NR_024056.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in an internal exon in the 3' region, compared to variant 1.
      Source sequence(s)
      AC006116, BC089419, BX647919, DA095148, DA311525

    4. NR_024057.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate internal exon in the 3' region, compared to variant 1.
      Source sequence(s)
      AC006116, BC089419, DA095148, DA311525
      Related
      ENST00000495307.5

    5. NR_033418.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript.
      Source sequence(s)
      AC006116, BC064603, BC089419, DA095148, DA311525
      Related
      ENST00000490123.5

    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
      56368099..56379828
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      59462491..59474231
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_194319.1: Suppressed sequence

      Description
      NM_194319.1: This RefSeq was permanently suppressed because it is now thought that this gene is a transcribed pseudogene.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5EBM4.2 GenPept UniProtKB/Swiss-Prot:Q5EBM4

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials