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LOC123956258 Sharpr-MPRA regulatory region 2529 [ Homo sapiens (human) ]

Gene ID: 123956258, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123956258
Gene description
Sharpr-MPRA regulatory region 2529
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 primed 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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC123956258 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (143395508..143396450)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (144750935..144751877)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (143092601..143093543)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 131 member B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26792 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:143077234-143078134 Neighboring gene FAM131B antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:143088659-143089259 Neighboring gene Sharpr-MPRA regulatory region 10434 Neighboring gene microRNA 6892 Neighboring gene zyxin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:143101922-143102436 Neighboring gene EPH receptor A1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:143106021-143106633 Neighboring gene EPHA1 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 12322 Neighboring gene taste 2 receptor member 62 pseudogene Neighboring gene taste 2 receptor member 60

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_chr7:143092601-143093311

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_078449.2 

    Range
    101..1043
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    143395508..143396450
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654714.1 Reference GRCh38.p14 PATCHES

    Range
    14872..15814
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    144750935..144751877
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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