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LOC124416847 Sharpr-MPRA regulatory region 6857 [ Homo sapiens (human) ]

Gene ID: 124416847, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124416847
Gene description
Sharpr-MPRA regulatory region 6857
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124416847 in Genome Data Viewer
Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (76336231..76336525)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (77210243..77210537)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (78095989..78096283)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene leucine rich melanocyte differentiation associated Neighboring gene uncharacterized LOC124902462 Neighboring gene Sharpr-MPRA regulatory region 11048 Neighboring gene uncharacterized LOC112268057 Neighboring gene VISTA enhancer hs1683 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:78192871-78193568 Neighboring gene VISTA enhancer hs1434 Neighboring gene Sharpr-MPRA regulatory region 3593 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:78383798-78384997 Neighboring gene VISTA enhancer hs748 Neighboring gene NANOG hESC enhancer GRCh37_chr10:78538831-78539723 Neighboring gene OCT4 hESC enhancer GRCh37_chr10:78568996-78569497 Neighboring gene NANOG hESC enhancer GRCh37_chr10:78582741-78583242 Neighboring gene ATP synthase membrane subunit c locus 1 pseudogene 8 Neighboring gene uncharacterized LOC124902466 Neighboring gene KCNMA1 antisense RNA 1 Neighboring gene potassium calcium-activated channel subfamily M alpha 1

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_079068.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    76336231..76336525
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    77210243..77210537
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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Other Literature Sources
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