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LOC124403913 Sharpr-MPRA regulatory region 15561 [ Homo sapiens (human) ]

Gene ID: 124403913, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124403913
Gene description
Sharpr-MPRA regulatory region 15561
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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
10p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (13740369..13740663)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (13753441..13753735)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (13782369..13782663)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene FERM domain containing 4A Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13749502-13750237 Neighboring gene uncharacterized LOC124902379 Neighboring gene uncharacterized LOC105376426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13753704-13754570 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:13754571-13755435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2158 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13770188-13771042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3063 Neighboring gene RNA, 5S ribosomal pseudogene 301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3064 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:13799977-13801176 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13830309-13830899 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:13868526-13868712 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13912798-13913451 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13922897-13923786 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13923787-13924677 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13924678-13925567 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3067 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:13946263-13946779 Neighboring gene nuclear transport factor 2 pseudogene 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:13984208-13984392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:13987981-13988481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:14013273-14014244 Neighboring gene uncharacterized LOC105376425

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_078993.1 

    Range
    101..395
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    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
    13740369..13740663
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    13753441..13753735
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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Other Literature Sources
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