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LOC125371492 Sharpr-MPRA regulatory region 11250 [ Homo sapiens (human) ]

Gene ID: 125371492, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371492
Gene description
Sharpr-MPRA regulatory region 11250
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 non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, May 2022]
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Genomic context

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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (17991320..17991614)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (18125398..18125692)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10363 Neighboring gene coiled-coil domain containing 124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18062016-18062634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18062635-18063252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18063253-18063870 Neighboring gene MPRA-validated peak3398 silencer Neighboring gene potassium calcium-activated channel subfamily N member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18073163-18073735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18076903-18077620 Neighboring gene RNA, 5S ribosomal pseudogene 468 Neighboring gene MPRA-validated peak3399 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18095189-18095870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18098837-18099338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18099339-18099838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18107595-18108096 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14293 Neighboring gene arrestin domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18124072-18124572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14294 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18132997-18133546 Neighboring gene CS pseudogene 3

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_080793.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    17991320..17991614
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    18125398..18125692
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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