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LOC124849288 Sharpr-MPRA regulatory region 8404 [ Homo sapiens (human) ]

Gene ID: 124849288, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124849288
Gene description
Sharpr-MPRA regulatory region 8404
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. A subregion was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes two accessible chromatin subregions that were validated as silencers based on their ability to repress 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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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (131895949..131896348)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (131940670..131941069)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903058 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132347237-132347900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132348565-132349228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132352369-132352965 Neighboring gene uncharacterized LOC124903059 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5102 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132381351-132382148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132384711-132385228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132385229-132385746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132385901-132386674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132386675-132387447 Neighboring gene unc-51 like autophagy activating kinase 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7373 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:132409300-132410176 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5106 Neighboring gene PUS1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5107 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25941 Neighboring gene pseudouridine synthase 1 Neighboring gene Sharpr-MPRA regulatory region 9670

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 5103
  • ATAC-STARR-seq lymphoblastoid silent region 5104

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_079863.2 

    Range
    101..500
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    131895949..131896348
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    131940670..131941069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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