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LOC121627809 Sharpr-MPRA regulatory region 12965 [ Homo sapiens (human) ]

Gene ID: 121627809, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627809
Gene description
Sharpr-MPRA regulatory region 12965
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. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State8:EnhW, candidate weak enhancer and open chromatin). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 8:EnhW). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (75581028..75581322)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (76474196..76474490)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (73577109..73577403)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 12010 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8971 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:73521300-73521484 Neighboring gene tRNA splicing endonuclease subunit 54 Neighboring gene LLGL scribble cell polarity complex component 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73537609-73538426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73540787-73541589 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73548510-73549090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73553000-73553936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73553937-73554872 Neighboring gene Sharpr-MPRA regulatory region 3602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12767 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12769 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73583697-73584530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73584531-73585362 Neighboring gene myosin XVB Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73628586-73629266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73629267-73629946 Neighboring gene RecQ like helicase 5 Neighboring gene small integral membrane protein 5

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

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)

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_074999.1 

    Range
    101..395
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    75581028..75581322
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    76474196..76474490
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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