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LOC124310668 Sharpr-MPRA regulatory region 491 [ Homo sapiens (human) ]

Gene ID: 124310668, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310668
Gene description
Sharpr-MPRA regulatory region 491
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 H3K27ac and H3K4me1 histone modifications. 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 K562 erythroleukemia cells (group: K562 Repressive 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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See LOC124310668 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (130451307..130452016)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (142656271..142656979)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (133327109..133327403)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene hemicentin 2 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133296398-133297200 Neighboring gene uncharacterized LOC107987134 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133297201-133298001 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133302089-133302636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133303731-133304276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133321151-133321818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133322488-133323155 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133328870-133329370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133342170-133342798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133346469-133347206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133347207-133347943 Neighboring gene VISTA enhancer hs1328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133355453-133356208 Neighboring gene argininosuccinate synthase 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:133373167-133373668 Neighboring gene Sharpr-MPRA regulatory region 5386 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:133380533-133381032 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:133381216-133382062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133394336-133394851 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133397629-133398376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133401147-133401648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133401649-133402148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133402913-133403413 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:133420171-133420671 Neighboring gene uncharacterized LOC100272217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20402 Neighboring gene uncharacterized LOC124902286 Neighboring gene far upstream element binding protein 3

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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133326694-133327395

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_078949.2 

    Range
    101..810
    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
    130451307..130452016
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    142656271..142656979
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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