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LOC113875007 Sharpr-MPRA regulatory region 4549 [ Homo sapiens (human) ]

Gene ID: 113875007, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113875007
Gene description
Sharpr-MPRA regulatory region 4549
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 K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin), with weaker activation in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Dec 2018]
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Genomic context

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Location:
Xq
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (123217138..123217432)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (121525834..121526128)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (122350989..122351283)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U3 Neighboring gene MPRA-validated peak7421 silencer Neighboring gene mitochondrial ribosome recycling factor pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:122364489-122365428 Neighboring gene glutamate ionotropic receptor AMPA type subunit 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:122416639-122417140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:122451941-122452481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:122525440-122525940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29908 Neighboring gene cytochrome c oxidase subunit NDUFA4-like Neighboring gene H3 histone pseudogene 47

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_063195.1 

    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    123217138..123217432
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    121525834..121526128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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