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LOC125146410 Sharpr-MPRA regulatory region 2706 [ Homo sapiens (human) ]

Gene ID: 125146410, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125146410
Gene description
Sharpr-MPRA regulatory region 2706
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (11574513..11574807)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (11610623..11610912)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371082 Neighboring gene mitochondrial ribosomal protein L18 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11480804-11481686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11483724-11484478 Neighboring gene putative uncharacterized protein LOC400499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11507777-11508748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11550335-11550854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11550855-11551372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10445 Neighboring gene uncharacterized LOC101927131 Neighboring gene uncharacterized LOC124903807 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11564147-11564648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11588027-11589023 Neighboring gene Sharpr-MPRA regulatory region 8116 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:11592015-11592563 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11595297-11596228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11610059-11610587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11612139-11612638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11620432-11621366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11621367-11622300 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr16:11637410-11638225 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11654074-11654928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:11656029-11656658 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11657289-11657918 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:11657919-11658546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11665841-11666778 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10450 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7204 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7205 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11688769-11689642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11689643-11690514 Neighboring gene lipopolysaccharide induced TNF factor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11697089-11697681 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11699131-11699630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10451 Neighboring gene Sharpr-MPRA regulatory region 4417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11708187-11708794 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11708795-11709402 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11715855-11716623 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11720940-11721474 Neighboring gene uncharacterized LOC124903643 Neighboring gene Sharpr-MPRA regulatory region 8349 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:11735633-11736296 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11766535-11767354 Neighboring gene thioredoxin domain containing 11 Neighboring gene stannin

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

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_080339.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    11574513..11574807
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    11610623..11610912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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