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LOC121331337 Sharpr-MPRA regulatory region 563 [ Homo sapiens (human) ]

Gene ID: 121331337, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121331337
Gene description
Sharpr-MPRA regulatory region 563
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 an 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 DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). The same subregion also displayed repressive activity by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (97307127..97307864)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (109479072..109479809)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (100069409..100069703)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ankyrin repeat domain 18C, pseudogene Neighboring gene SUGT1P4-STRA6LP-CCDC180 readthrough Neighboring gene SUGT1P4-STRA6LP readthrough Neighboring gene Sharpr-MPRA regulatory region 7929 Neighboring gene SUGT1 pseudogene 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100033649-100034149 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100057407-100057584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20098 Neighboring gene STRA6 like, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100074371-100074871 Neighboring gene coiled-coil domain containing 180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28659 Neighboring gene microRNA 1302-8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100148028-100148534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100148535-100149040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100150291-100150855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28661 Neighboring gene uncharacterized LOC286359

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_chr9:100069646-100070146

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_074361.2 

    Range
    101..838
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    97307127..97307864
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    109479072..109479809
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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