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LOC124421489 Sharpr-MPRA regulatory region 886 [ Homo sapiens (human) ]

Gene ID: 124421489, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124421489
Gene description
Sharpr-MPRA regulatory region 886
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. Another subregion was validated as a repressive element 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 Repressive non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
11p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (12092222..12092909)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (12184078..12184765)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (12113769..12114063)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2547 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:12087483-12088682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12114457-12114957 Neighboring gene long intergenic non-protein coding RNA 2989 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:12125283-12125783 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12132043-12132746 Neighboring gene GATA motif-containing MPRA enhancer 176/177 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12158230-12158730 Neighboring gene microtubule associated monooxygenase, calponin and LIM domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12160461-12161004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12161005-12161546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12184971-12185470 Neighboring gene Sharpr-MPRA regulatory region 10887 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12200287-12201161 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12203881-12204381 Neighboring gene microRNA 6124 Neighboring gene Sharpr-MPRA regulatory region 12121 Neighboring gene uncharacterized LOC124902634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12238418-12238918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12238919-12239419

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K4me1 hESC enhancer GRCh37_chr11:12113956-12114456

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_079178.2 

    Range
    101..788
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    12092222..12092909
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    12184078..12184765
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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