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LOC121587590 Sharpr-MPRA regulatory region 12086 [ Homo sapiens (human) ]

Gene ID: 121587590, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121587590
Gene description
Sharpr-MPRA regulatory region 12086
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121587590 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (39359116..39359410)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (40223028..40223322)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (37515369..37515663)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene transcription factor CP2-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37400607-37401181 Neighboring gene F-box and leucine rich repeat protein 20 Neighboring gene microRNA 548BC Neighboring gene MPRA-validated peak2834 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:37489325-37489835 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:37493495-37494252 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8453 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8454 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:37557132-37557424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8455 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8456 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:37558864-37559028 Neighboring gene mediator complex subunit 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:37618166-37619365 Neighboring gene U6 spliceosomal RNA Neighboring gene cyclin dependent kinase 12

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_074975.1 

    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
    39359116..39359410
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    40223028..40223322
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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