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LOC112469006 Sharpr-MPRA regulatory region 3054 [ Homo sapiens (human) ]

Gene ID: 112469006, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112469006
Gene description
Sharpr-MPRA regulatory region 3054
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in K562 cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (57145657..57145951)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (62941931..62942225)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (57179569..57179863)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57023277-57023776 Neighboring gene Sharpr-MPRA regulatory region 12884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10869 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:57033747-57034248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10871 Neighboring gene NLR family CARD domain containing 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57060363-57060881 Neighboring gene CFAP69 pseudogene 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10879 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10880 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:57095254-57096453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57103335-57104060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57104061-57104785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7519 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7520 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57137039-57137994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57139274-57139873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10882 Neighboring gene copine 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7523 Neighboring gene Sharpr-MPRA regulatory region 6435 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57183845-57184634 Neighboring gene proteasome activator subunit 3 interacting protein 1 Neighboring gene NANOG hESC enhancer GRCh37_chr16:57212532-57213113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7524 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr16:57220937-57221581 Neighboring gene ring finger and SPRY domain containing 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10885

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. 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)

General gene information

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Other Names

  • ReSE screen-validated silencer GRCh37_chr16:57179572-57179777

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_056833.1 

    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
    57145657..57145951
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    62941931..62942225
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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