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LOC129389244 MPRA-validated peak5138 silencer [ Homo sapiens (human) ]

Gene ID: 129389244, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129389244
Gene description
MPRA-validated peak5138 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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Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (156247564..156247764)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (159592688..159592888)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ferritin heavy chain 1 pseudogene 21 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:157027553-157028054 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:157032791-157033399 Neighboring gene uncharacterized LOC102724785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15771 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74949 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:157210831-157211442 Neighboring gene uncharacterized LOC105377508 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74995 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75023 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:157426362-157427068 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75051 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:157519367-157520566 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:157521211-157521946 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:157526591-157527116 Neighboring gene NANOG hESC enhancer GRCh37_chr4:157555350-157555851 Neighboring gene long intergenic non-protein coding RNA 2272

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

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_154875.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    156247564..156247764
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    159592688..159592888
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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