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LOC125146387 Sharpr-MPRA regulatory region 12742 [ Homo sapiens (human) ]

Gene ID: 125146387, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125146387
Gene description
Sharpr-MPRA regulatory region 12742
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 DNase unmatched - State 8:EnhW, candidate weak enhancer and 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 (4282448..4282742)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (4309785..4310080)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4302672-4303294 Neighboring gene long intergenic non-protein coding RNA 1569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10336 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7148 Neighboring gene uncharacterized LOC124903634 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4314566-4315209 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4315210-4315854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4321241-4322217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10338 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4323195-4324170 Neighboring gene transcription factor AP-4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4336703-4337204 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4337205-4337704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10339 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4340142-4340760 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4344437-4345096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4346736-4347609 Neighboring gene Sharpr-MPRA regulatory region 643 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4355312-4355824 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:4362415-4362646 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr16:4364183-4364695 and GRCh37_chr16:4364696-4365208 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4367330-4367980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4367981-4368630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4372394-4373179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4374751-4375535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4378569-4379569 Neighboring gene GLIS family zinc finger 2 Neighboring gene GLIS2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4389543-4390289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4390290-4391035 Neighboring gene CORO7-PAM16 readthrough Neighboring gene MPRA-validated peak2471 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4397350-4397850 Neighboring gene presequence translocase associated motor 16

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_080316.1 

    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
    4282448..4282742
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    4309785..4310080
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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