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LOC125446234 Sharpr-MPRA regulatory region 3662 [ Homo sapiens (human) ]

Gene ID: 125446234, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125446234
Gene description
Sharpr-MPRA regulatory region 3662
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 DNase matched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [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 (39328104..39328398)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39798754..39799048)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39712838-39713726 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39714617-39715506 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39715507-39716396 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39716397-39717285 Neighboring gene small nucleolar RNA, C/D box 139 Neighboring gene ribosomal protein L3 Neighboring gene small nucleolar RNA, C/D box 43 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39753396-39753924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39755840-39756638 Neighboring gene synaptogyrin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39757867-39758453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39758454-39759039 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39769919-39770434 Neighboring gene Sharpr-MPRA regulatory region 1576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19046 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13751 Neighboring gene TGF-beta activated kinase 1 (MAP3K7) binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39811177-39811678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39811679-39812178 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39824885-39825527 Neighboring gene uncharacterized LOC100506472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39829518-39830236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39830237-39830954

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_081173.1 

    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
    39328104..39328398
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    39798754..39799048
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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