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    LOC129389670 MPRA-validated peak6179 silencer [ Homo sapiens (human) ]

    Gene ID: 129389670, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC129389670
    Gene description
    MPRA-validated peak6179 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 LOC129389670 in Genome Data Viewer
    Location:
    chromosome: 6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (143706358..143706558)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (144899073..144899273)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (144027495..144027695)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378035 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:143832494-143833156 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:143833157-143833817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17629 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25203 Neighboring gene PHACTR2 antisense RNA 1 Neighboring gene phosphatase and actin regulator 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17630 Neighboring gene MPRA-validated peak6177 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:143958702-143959245 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:143998446-143999294 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:144059920-144060420 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144065167-144065836 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:144067178-144067848 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144067849-144068518 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144068519-144069188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25206 Neighboring gene MPRA-validated peak6180 silencer Neighboring gene MPRA-validated peak6181 silencer Neighboring gene LTV1 ribosome biogenesis factor Neighboring gene zinc finger C2HC-type containing 1B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25207

    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_155300.1 

      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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      143706358..143706558
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      144899073..144899273
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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