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LOC125424387 Sharpr-MPRA regulatory region 11316 [ Homo sapiens (human) ]

Gene ID: 125424387, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125424387
Gene description
Sharpr-MPRA regulatory region 11316
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, May 2022]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (20238546..20238840)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (20618338..20618632)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905083 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20210507-20211174 Neighboring gene uncharacterized LOC105372863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20218512-20219305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20225493-20226085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20230230-20230822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18673 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:20234375-20234965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20235693-20236294 Neighboring gene reticulon 4 receptor Neighboring gene microRNA 1286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20243726-20244270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:20254685-20255373 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13486 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20262187-20262687 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20269715-20270454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20270455-20271195 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20271196-20271935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20280047-20280548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:20285530-20286031 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13489 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13492 Neighboring gene proline dehydrogenase like, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20300941-20301496

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

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_081122.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    20238546..20238840
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    20618338..20618632
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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