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LOC122861243 Sharpr-MPRA regulatory region 14969 [ Homo sapiens (human) ]

Gene ID: 122861243, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122861243
Gene description
Sharpr-MPRA regulatory region 14969
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122861243 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (174761881..174762175)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (175250590..175250884)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (175626609..175626903)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene WAS/WASL interacting protein family member 1 Neighboring gene uncharacterized LOC124907907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12128 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12129 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:175578156-175578368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:175594551-175595290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:175629201-175629700 Neighboring gene H3 histone pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:175646775-175647382 Neighboring gene cholinergic receptor nicotinic alpha 1 subunit Neighboring gene uncharacterized LOC124907908 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:175652041-175652856 Neighboring gene Sharpr-MPRA regulatory region 431 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:175660322-175661184 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:175661185-175662046 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:175679928-175680086 Neighboring gene chimerin 1 Neighboring gene Sharpr-MPRA regulatory region 13906 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:175778728-175779927 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:175788643-175789389 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:175789465-175790079 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:175790080-175790693 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:175828782-175829617 Neighboring gene MPRA-validated peak3936 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:175831556-175832392 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:175869279-175869825 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12131

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_077059.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    174761881..174762175
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    175250590..175250884
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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