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LOC125146408 Sharpr-MPRA regulatory region 4189 [ Homo sapiens (human) ]

Gene ID: 125146408, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125146408
Gene description
Sharpr-MPRA regulatory region 4189
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125146408 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (11234952..11235246)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (11271187..11271481)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene C-type lectin domain containing 16A Neighboring gene uncharacterized LOC105371081 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11234584-11235161 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11234005-11234583 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11235162-11235740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11238795-11239462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11268031-11268544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11275481-11276366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11276367-11277253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11291308-11291816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11290798-11291307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11292853-11293353 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:11295121-11296320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11296313-11297109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11304646-11305240 Neighboring gene uncharacterized LOC107984859 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10424 Neighboring gene CRISPRi-validated cis-regulatory element chr16.1224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10425 Neighboring gene uncharacterized LOC105371082 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11344039-11344246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7197 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7200 Neighboring gene heterogeneous nuclear ribonucleoprotein C pseudogene 4 Neighboring gene suppressor of cytokine signaling 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

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_080337.1 

    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
    11234952..11235246
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    11271187..11271481
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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