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LOC121079952 Sharpr-MPRA regulatory region 14586 [ Homo sapiens (human) ]

Gene ID: 121079952, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121079952
Gene description
Sharpr-MPRA regulatory region 14586
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Apr 2021]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (104189948..104190242)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (104698694..104698988)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (103525649..103525943)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379107 Neighboring gene uncharacterized LOC101930276 Neighboring gene MPRA-validated peak5381 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:103372498-103373042 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:103399302-103400266 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:103405398-103406312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:103415333-103415858 Neighboring gene RNA, U1 small nuclear 140, pseudogene Neighboring gene ncRNA involved in NHEJ oncogenic ligation efficiency Neighboring gene RNA, 7SL, cytoplasmic 255, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:103652082-103653281 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:103707754-103708953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:103739859-103740360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:103740361-103740860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:103787247-103787852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:103787853-103788456 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_80648 Neighboring gene uncharacterized LOC105379109 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:103985884-103986480 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:104089973-104090787

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_074170.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    104189948..104190242
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    104698694..104698988
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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