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LOC125446230 Sharpr-MPRA regulatory region 7746 [ Homo sapiens (human) ]

Gene ID: 125446230, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125446230
Gene description
Sharpr-MPRA regulatory region 7746
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 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jun 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 (37601562..37601856)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (38062840..38063134)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37957123-37957729 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37957730-37958337 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37958338-37958944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37959472-37959972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37959973-37960473 Neighboring gene CDC42 effector protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37963831-37964482 Neighboring gene HNF1 motif-containing MPRA enhancer 93 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37965972-37966480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37967120-37967620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37967621-37968121 Neighboring gene galectin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13687 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18977 Neighboring gene CRISPRi-validated cis-regulatory element chr22.1757 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:38005225-38005846 Neighboring gene golgi associated, gamma adaptin ear containing, ARF binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:38029311-38030184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18984 Neighboring gene Sharpr-MPRA regulatory region 10481 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13690 Neighboring gene SH3 domain binding protein 1 Neighboring gene PDXP 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_081169.1 

    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
    37601562..37601856
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    38062840..38063134
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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