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LOC125446236 Sharpr-MPRA regulatory region 14739 [ Homo sapiens (human) ]

Gene ID: 125446236, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125446236
Gene description
Sharpr-MPRA regulatory region 14739
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 5:Enh, candidate strong enhancer, 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:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (39534744..39535103)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (40005374..40005733)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19058 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39919051-39919552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19067 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19068 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:39927967-39928482 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:39928483-39928998 Neighboring gene ribosomal protein S19 binding protein 1 Neighboring gene activating transcription factor 4 Neighboring gene uncharacterized LOC124905120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39953934-39954532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39970777-39971278 Neighboring gene calcium voltage-gated channel subunit alpha1 I Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39987813-39988722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19072 Neighboring gene Sharpr-MPRA regulatory region 12417 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40022927-40023476 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40023477-40024025 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40030871-40031590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40047218-40048148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40051895-40052396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13763 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40059793-40060322

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 13761
  • ATAC-STARR-seq lymphoblastoid silent region 13762

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_081175.2 

    Range
    101..460
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    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    39534744..39535103
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    40005374..40005733
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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