U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC121838596 Sharpr-MPRA regulatory region 2571 [ Homo sapiens (human) ]

Gene ID: 121838596, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC121838596
Gene description
Sharpr-MPRA regulatory region 2571
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (68295352..68295708)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (62501788..62502144)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (68762069..68762363)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene RAD51 paralog B Neighboring gene uncharacterized LOC105370546 Neighboring gene VISTA enhancer hs1392 Neighboring gene RNA, 7SL, cytoplasmic 706, pseudogene Neighboring gene Sharpr-MPRA regulatory region 3110 Neighboring gene MPRA-validated peak2183 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8589 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8590 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:68698864-68700063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8592 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8593 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8594 Neighboring gene RNA, 7SL, cytoplasmic 108, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8595 Neighboring gene Sharpr-MPRA regulatory region 2611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8596 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8597 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8598 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8599 Neighboring gene Sharpr-MPRA regulatory region 10624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8606 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:68810048-68810732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5867 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:68830720-68831247 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:68831248-68831776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8607 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:68838900-68839755 Neighboring gene VISTA enhancer hs1688 Neighboring gene uncharacterized LOC101927971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:68863880-68864606 Neighboring gene ribosomal protein L7a pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8608

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 8601

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_075959.2 

    Range
    101..457
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    68295352..68295708
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    62501788..62502144
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases