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LOC125371437 Sharpr-MPRA regulatory region 13227 [ Homo sapiens (human) ]

Gene ID: 125371437, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371437
Gene description
Sharpr-MPRA regulatory region 13227
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 K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125371437 in Genome Data Viewer
Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (63220896..63221190)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (63425862..63426156)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13446 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:60805026-60805892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:60813108-60813608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:60813609-60814109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13452 Neighboring gene BCL2 apoptosis regulator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13462 Neighboring gene uncharacterized LOC124904379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13463 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:60881329-60881829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9522 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9523 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9524 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9525 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13467 Neighboring gene 3-ketodihydrosphingosine reductase Neighboring gene uncharacterized LOC124904317 Neighboring gene Sharpr-MPRA regulatory region 13815 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:61033863-61034810 Neighboring gene KDSR divergent transcript

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_080707.1 

    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    63220896..63221190
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    63425862..63426156
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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