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LOC123493316 Sharpr-MPRA regulatory region 14379 [ Homo sapiens (human) ]

Gene ID: 123493316, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123493316
Gene description
Sharpr-MPRA regulatory region 14379
Gene type
biological region
Feature type(s)
regulatory: 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 repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123493316 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (57837642..57837936)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (58666435..58666729)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (57133469..57133763)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901182 Neighboring gene lncRNA SMARCA2 (BRM) associated Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:56937789-56938367 Neighboring gene uncharacterized LOC101928505 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:56988450-56989649 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:56994597-56995101 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:57011915-57013114 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:57030843-57032042 Neighboring gene Sharpr-MPRA regulatory region 14061 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:57131079-57131587 Neighboring gene NANOG hESC enhancer GRCh37_chr5:57141460-57142040 Neighboring gene long intergenic non-protein coding RNA 2225 Neighboring gene Sharpr-MPRA regulatory region 13165 Neighboring gene uncharacterized LOC124901183 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:57363636-57364835

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_077740.1 

    Range
    101..395
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    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    57837642..57837936
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    58666435..58666729
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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