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LOC125146406 Sharpr-MPRA regulatory region 12638 [ Homo sapiens (human) ]

Gene ID: 125146406, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125146406
Gene description
Sharpr-MPRA regulatory region 12638
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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Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (10971532..10971826)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (11007503..11007797)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10391 Neighboring gene Rho GTPase activating protein 21 pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:10964767-10965966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10399 Neighboring gene class II major histocompatibility complex transactivator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10401 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10406 Neighboring gene Dexi homolog Neighboring gene C-type lectin domain containing 16A Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11066007-11066184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11073759-11074260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11074261-11074760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7196 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11099817-11100053 Neighboring gene NANOG hESC enhancer GRCh37_chr16:11101530-11102234 Neighboring gene Sharpr-MPRA regulatory region 10204 Neighboring gene ribosomal protein L7 pseudogene 46 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11144766-11145343 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11144189-11144765 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10412 Neighboring gene Sharpr-MPRA regulatory region 12604 Neighboring gene uncharacterized LOC105371081

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_080335.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    10971532..10971826
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    11007503..11007797
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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