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LOC113002596 Sharpr-MPRA regulatory region 10583 [ Homo sapiens (human) ]

Gene ID: 113002596, updated on 17-Sep-2024

Summary

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Gene symbol
LOC113002596
Gene description
Sharpr-MPRA regulatory region 10583
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Aug 2018]
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Genomic context

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See LOC113002596 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (95924725..95925019)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (96425971..96426265)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (95260429..95260723)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901029 Neighboring gene uncharacterized LOC105379091 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:95197672-95198871 Neighboring gene NANOG hESC enhancer GRCh37_chr5:95199127-95199628 Neighboring gene long intergenic non-protein coding RNA 1554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16189 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:95297407-95298164 Neighboring gene uncharacterized LOC101929710 Neighboring gene uncharacterized LOC105379096 Neighboring gene Sharpr-MPRA regulatory region 2569 Neighboring gene elongation factor for RNA polymerase II 2 Neighboring gene fatty acid binding protein 5 pseudogene 5 Neighboring gene calpastatin Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:95401160-95402062

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 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_061607.1 

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

    Range
    95924725..95925019
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    96425971..96426265
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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