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LOC124416893 Sharpr-MPRA regulatory region 15234 [ Homo sapiens (human) ]

Gene ID: 124416893, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124416893
Gene description
Sharpr-MPRA regulatory region 15234
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 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124416893 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 (102306072..102306366)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (103191032..103191326)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (104065829..104066123)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2751 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:103989615-103989783 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2753 Neighboring gene ELOVL fatty acid elongase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3926 Neighboring gene paired like homeodomain 3 Neighboring gene golgi brefeldin A resistant guanine nucleotide exchange factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104029238-104029738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104029739-104030239 Neighboring gene Sharpr-MPRA regulatory region 13217 Neighboring gene uncharacterized LOC107984263 Neighboring gene MPRA-validated peak1080 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:104147078-104147638 Neighboring gene NANOG hESC enhancer GRCh37_chr10:104151284-104151791 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:104151792-104152298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3929 Neighboring gene Sharpr-MPRA regulatory region 13585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104160632-104161328 Neighboring gene nuclear factor kappa B subunit 2

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_079108.1 

    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
    102306072..102306366
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    103191032..103191326
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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