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LOC129389239 MPRA-validated peak5125 silencer [ Homo sapiens (human) ]

Gene ID: 129389239, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129389239
Gene description
MPRA-validated peak5125 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 (141867763..141867963)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (145185111..145185311)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:142501441-142502640 Neighboring gene long intergenic non-protein coding RNA 2276 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:142546083-142546797 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:142628696-142629196 Neighboring gene interleukin 15 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:142803658-142804281 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:142804282-142804904 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:142823512-142824114 Neighboring gene inositol polyphosphate-4-phosphatase type II B Neighboring gene ribosomal protein L5 pseudogene 13 Neighboring gene LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated pseudogene 4

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_154870.1 

    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
    141867763..141867963
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    145185111..145185311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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