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LOC114004404 Sharpr-MPRA regulatory region 3236 [ Homo sapiens (human) ]

Gene ID: 114004404, updated on 17-Sep-2024

Summary

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Gene symbol
LOC114004404
Gene description
Sharpr-MPRA regulatory region 3236
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 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 Repressive DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with 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 HepG2 cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC114004404 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (69232897..69233191)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (70411568..70411862)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (69942789..69943083)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901511 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:69404211-69404763 Neighboring gene Sharpr-MPRA regulatory region 12937 Neighboring gene uncharacterized LOC124901492 Neighboring gene adhesion G protein-coupled receptor B3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94316 Neighboring gene Sharpr-MPRA regulatory region 12106 Neighboring gene Sharpr-MPRA regulatory region 1724 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:69890327-69891526 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:69925706-69926680 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:70118423-70119622 Neighboring gene NANOG hESC enhancer GRCh37_chr6:70141628-70142137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:70154657-70155166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:70155167-70155674 Neighboring gene Sharpr-MPRA regulatory region 1352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:70364977-70365478 Neighboring gene MPRA-validated peak5886 silencer Neighboring gene uncharacterized LOC124901337 Neighboring gene LMBR1 domain containing 1 Neighboring gene nucleophosmin 1 pseudogene 37 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 42

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_chr6:69942916-69943081

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_063904.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    69232897..69233191
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    70411568..70411862
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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