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LOC121725148 Sharpr-MPRA regulatory region 15147 [ Homo sapiens (human) ]

Gene ID: 121725148, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725148
Gene description
Sharpr-MPRA regulatory region 15147
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). 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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Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (61181976..61182270)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (61225160..61225454)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (61167649..61167943)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene fragile histidine triad diadenosine triphosphatase Neighboring gene uncharacterized LOC124906244 Neighboring gene uncharacterized LOC105377111 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:61015791-61016990 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:61027375-61028574 Neighboring gene Sharpr-MPRA regulatory region 1919 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:61126817-61127339 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:61127340-61127863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20025 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20027 Neighboring gene Sharpr-MPRA regulatory region 9847 Neighboring gene uncharacterized LOC124909387 Neighboring gene uncharacterized LOC105377114 Neighboring gene uncharacterized LOC105377115 Neighboring gene Sharpr-MPRA regulatory region 1523

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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 20021

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_075617.1 

    Range
    101..395
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    61181976..61182270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    61225160..61225454
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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