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LOC123956214 Sharpr-MPRA regulatory region 9016 [ Homo sapiens (human) ]

Gene ID: 123956214, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956214
Gene description
Sharpr-MPRA regulatory region 9016
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 associates with the OCT4 transcription factor and is marked by the H3K27ac 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 21:Repr, strong Polycomb repression). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (116522749..116523609)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (117837812..117838640)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (116163369..116163663)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986838 Neighboring gene greater CFTR locus negative regulatory element NR1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:116082532-116083731 Neighboring gene greater CFTR locus negative regulatory element CR2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:116138807-116139308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18556 Neighboring gene Sharpr-MPRA regulatory region 4219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18557 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18558 Neighboring gene Sharpr-MPRA regulatory region 15503 Neighboring gene caveolin 2 Neighboring gene caveolin 1 Neighboring gene Sharpr-MPRA regulatory region 6449 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18559 Neighboring gene greater CFTR locus negative regulatory element NR2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26535 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26536 Neighboring gene cytosolic oncogenic antisense to MET transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26537 Neighboring gene MPRA-validated peak6696 silencer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:116273493-116274692 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18560 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18561 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18562 Neighboring gene greater CFTR locus negative regulatory element CR3 Neighboring gene MET proto-oncogene, receptor tyrosine kinase

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

  • OCT4-H3K27ac hESC enhancer GRCh37_chr7:116162803-116163443

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_078408.2 

    Range
    101..961
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    116522749..116523609
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    117837812..117838640
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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