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LOC129390553 MPRA-validated peak1943 silencer [ Homo sapiens (human) ]

Gene ID: 129390553, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390553
Gene description
MPRA-validated peak1943 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 LOC129390553 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (109396590..109396790)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (109371498..109371698)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (109834395..109834595)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109722785-109723628 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:109725470-109725629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109725794-109726403 Neighboring gene MPRA-validated peak1938 silencer Neighboring gene Sharpr-MPRA regulatory region 9197 Neighboring gene forkhead box N4 Neighboring gene MPRA-validated peak1941 silencer Neighboring gene myosin IH Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6985 Neighboring gene long intergenic non-protein coding RNA 1486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109871570-109872074 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109896331-109897136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109897944-109898749 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109898750-109899556 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109900363-109901169 Neighboring gene potassium channel tetramerization domain containing 10 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:109914018-109914753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6986 Neighboring gene ubiquitin protein ligase E3B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109976965-109977466 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109978915-109979477

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_156183.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    109396590..109396790
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    109371498..109371698
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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