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LOC124153159 Sharpr-MPRA regulatory region 2659 [ Homo sapiens (human) ]

Gene ID: 124153159, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124153159
Gene description
Sharpr-MPRA regulatory region 2659
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124153159 in Genome Data Viewer
Location:
8p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (42658726..42659020)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (42926777..42927071)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (42513869..42514163)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancers GRCh37_chr8:42248902-42249402 and GRCh37_chr8:42249403-42249903 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:42258699-42258918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27311 Neighboring gene voltage dependent anion channel 3 Neighboring gene solute carrier family 20 member 2 Neighboring gene Sharpr-MPRA regulatory region 15103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:42331955-42332466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:42332467-42332978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:42333451-42333976 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:42333977-42334500 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:42350219-42351086 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:42359656-42360855 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19157 Neighboring gene Sharpr-MPRA regulatory region 9023 Neighboring gene NANOG hESC enhancer GRCh37_chr8:42409514-42410035 Neighboring gene small integral membrane protein 19 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:42516917-42517417 Neighboring gene uncharacterized LOC124900250 Neighboring gene uncharacterized LOC105379396 Neighboring gene cholinergic receptor nicotinic beta 3 subunit

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

See Variation Viewer (GRCh37.p13)

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_078547.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    42658726..42659020
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    42926777..42927071
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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