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LOC122757923 Sharpr-MPRA regulatory region 382 [ Homo sapiens (human) ]

Gene ID: 122757923, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122757923
Gene description
Sharpr-MPRA regulatory region 382
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 21:Repr, strong Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Sep 2021]
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Genomic context

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See LOC122757923 in Genome Data Viewer
Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (41938369..41938663)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (41943853..41944147)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (42165509..42165803)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1913 Neighboring gene MPRA-validated peak3674 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15625 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:42157683-42158882 Neighboring gene uncharacterized LOC124905996 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:42164451-42165045 Neighboring gene long intergenic non-protein coding RNA 1914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:42166828-42167422 Neighboring gene long intergenic non-protein coding RNA 2898 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42175498-42176148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11392 Neighboring gene VISTA enhancer hs2553 Neighboring gene uncharacterized LOC105374517 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_58491 Neighboring gene Sharpr-MPRA regulatory region 7749 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:42220647-42221044 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:42222752-42223418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11393 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:42259331-42259881 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42273538-42274041 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42274042-42274546 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11397 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15635 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:42276763-42277264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:42279935-42280650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42280651-42281365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:42285233-42285733 Neighboring gene protein kinase domain containing, cytoplasmic

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_076915.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    41938369..41938663
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    41943853..41944147
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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