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LOC129388553 MPRA-validated peak293 silencer [ Homo sapiens (human) ]

Gene ID: 129388553, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388553
Gene description
MPRA-validated peak293 silencer
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC129388553 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (76843950..76844150)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (76681594..76681794)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (77309635..77309835)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr1:77231962-77232537 Neighboring gene RNA, U6 small nuclear 161, pseudogene Neighboring gene long intergenic non-protein coding RNA 2567 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:77319872-77320409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1212 Neighboring gene ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5 Neighboring gene NANOG hESC enhancer GRCh37_chr1:77365662-77366201 Neighboring gene NANOG hESC enhancer GRCh37_chr1:77426151-77426652 Neighboring gene MPRA-validated peak295 silencer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:77463853-77465052 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:77489814-77490314 Neighboring gene MPRA-validated peak297 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1213 Neighboring gene microRNA 7156 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class K Neighboring gene ribosomal protein L17 pseudogene 6

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 1211

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_154187.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    76843950..76844150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    76681594..76681794
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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