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    LOC108254667 PHF20 intron CAGE-defined high expression enhancer [ Homo sapiens (human) ]

    Gene ID: 108254667, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC108254667
    Gene description
    PHF20 intron CAGE-defined high expression enhancer
    Gene type
    biological region
    Feature type(s)
    misc_feature: CAGE_cluster
    regulatory: enhancer
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This genomic region is located in an intron of the PHF20 (PHD finger protein 20) gene. It was defined as a high expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE). It was validated as a functional enhancer by reporter assays in both HeLa and HepG2 cells. [provided by RefSeq, Jun 2016]
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    Genomic context

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    See LOC108254667 in Genome Data Viewer
    Location:
    20q11.22-q11.23
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (35875429..35875988)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (37596405..37596964)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (34463351..34463910)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904972 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12864 Neighboring gene Sharpr-MPRA regulatory region 2555 Neighboring gene PHD finger protein 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17798 Neighboring gene MPRA-validated peak4203 silencer Neighboring gene COX7B pseudogene 2 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 16 Neighboring gene RNA, U4 small nuclear 40, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See Variation Viewer (GRCh37.p13)

    General gene information

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    Other Names

    • PHF20 intron high CAGE FANTOM5 enhancer

    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.

    Genomic

    1. NG_051013.1 

      Range
      101..660
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      35875429..35875988
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      37596405..37596964
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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