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LOC123833524 Sharpr-MPRA regulatory region 9187 [ Homo sapiens (human) ]

Gene ID: 123833524, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123833524
Gene description
Sharpr-MPRA regulatory region 9187
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 non-DNase unmatched - State 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (111812166..111812460)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (112995249..112995543)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (112133369..112133663)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377944 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111982565-111983248 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111983249-111983930 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111983931-111984612 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:111998453-111999376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:112003973-112004474 Neighboring gene uncharacterized LOC105377945 Neighboring gene FYN proto-oncogene, Src family tyrosine kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24951 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:112051720-112052606 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:112052607-112053491 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24952 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:112072171-112072743 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:112085712-112086288 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17480 Neighboring gene Sharpr-MPRA regulatory region 12906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24957 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17481 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:112194227-112194726 Neighboring gene uncharacterized LOC102724646 Neighboring gene NANOG hESC enhancer GRCh37_chr6:112205254-112205757 Neighboring gene NANOG hESC enhancer GRCh37_chr6:112210097-112211042 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:112229311-112229997 Neighboring gene long intergenic non-protein coding RNA 2527

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_078178.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    111812166..111812460
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    112995249..112995543
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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