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    LOC129390055 MPRA-validated peak7183 silencer [ Homo sapiens (human) ]

    Gene ID: 129390055, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC129390055
    Gene description
    MPRA-validated peak7183 silencer
    Gene type
    biological region
    Feature type(s)
    regulatory: silencer
    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 was identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. It was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. [provided by RefSeq, Apr 2023]
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    Genomic context

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    See LOC129390055 in Genome Data Viewer
    Location:
    chromosome: 8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (134409653..134409853)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (135527618..135527818)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (135421896..135422096)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene MIA SH3 domain ER export factor 2 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135180517-135181018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135181019-135181518 Neighboring gene uncharacterized LOC124902070 Neighboring gene Sharpr-MPRA regulatory region 13712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19567 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135469463-135469963 Neighboring gene NANOG hESC enhancer GRCh37_chr8:135512751-135513262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:135534207-135534774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28012 Neighboring gene zinc finger and AT-hook domain containing Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:135593335-135594534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28016 Neighboring gene ZFAT antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135697807-135698308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135698309-135698808 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:135698888-135699054 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28019 Neighboring gene NANOG hESC enhancer GRCh37_chr8:135721671-135722354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28021 Neighboring gene uncharacterized LOC124902072

    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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, 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)

    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_155685.1 

      Range
      101..301
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      134409653..134409853
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      135527618..135527818
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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