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LOC123575668 Sharpr-MPRA regulatory region 1219 [ Homo sapiens (human) ]

Gene ID: 123575668, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575668
Gene description
Sharpr-MPRA regulatory region 1219
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 repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (11277396..11277690)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (11145350..11145644)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (11277629..11277923)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene endogenous retrovirus group FRD member 1, envelope Neighboring gene small integral membrane protein 13 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:11126939-11127440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23978 Neighboring gene Sharpr-MPRA regulatory region 2452 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:11185257-11186456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11189930-11190701 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11190702-11191472 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11195391-11196257 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11196258-11197123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23979 Neighboring gene neural precursor cell expressed, developmentally down-regulated 9 Neighboring gene uncharacterized LOC124901256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16911 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23980 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23983 Neighboring gene uncharacterized LOC105374925 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11298822-11299579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23984 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:11344190-11345389 Neighboring gene Sharpr-MPRA regulatory region 10259 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:11370467-11370968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:11370969-11371468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23985 Neighboring gene uncharacterized LOC105374927

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 23981

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_077927.1 

    Range
    101..395
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    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
    11277396..11277690
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    11145350..11145644
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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