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LOC124625899 Sharpr-MPRA regulatory region 11326 [ Homo sapiens (human) ]

Gene ID: 124625899, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124625899
Gene description
Sharpr-MPRA regulatory region 11326
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 non-DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). 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:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (8390543..8390847)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (8404528..8404832)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene small nuclear ribonucleoprotein polypeptide C pseudogene 7 Neighboring gene 40S ribosomal protein S24-like Neighboring gene long intergenic non-protein coding RNA 937 Neighboring gene RPS3A pseudogene 43 Neighboring gene uncharacterized LOC124906977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:8549829-8550330 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:8550331-8550830 Neighboring gene VPS51 pseudogene 3 Neighboring gene olfactory receptor family 7 subfamily E member 140 pseudogene

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 4214
  • ATAC-STARR-seq lymphoblastoid silent region 4215

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_079581.2 

    Range
    101..405
    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
    8390543..8390847
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    8404528..8404832
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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