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LOC124909516 Sharpr-MPRA regulatory region 8978 [ Homo sapiens (human) ]

Gene ID: 124909516, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124909516
Gene description
Sharpr-MPRA regulatory region 8978
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 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 8:EnhW, candidate weak enhancer and 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]
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Genomic context

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See LOC124909516 in Genome Data Viewer
Location:
13q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (98445835..98446129)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (97653626..97653924)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene FERM, ARH/RhoGEF and pleckstrin domain protein 1 Neighboring gene uncharacterized LOC105370327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7899 Neighboring gene FARP1 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 11628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99115971-99116472 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:99128412-99129611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99133110-99133610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7905 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99136594-99137285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7908 Neighboring gene serine/threonine kinase 24 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99148205-99149039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7911 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99159381-99159980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99158181-99158780 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99158781-99159380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7913 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99172581-99173082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99188643-99189506 Neighboring gene Sharpr-MPRA regulatory region 8410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99220135-99220636 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr13:99222661-99223860 Neighboring gene Sharpr-MPRA regulatory region 9599 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5457 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5458 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7919 Neighboring gene STK24 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7920 Neighboring gene NUS1 pseudogene 4

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 active region 7900

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_080027.1 

    Range
    101..395
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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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    98445835..98446129
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    97653626..97653924
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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