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LOC125446258 Sharpr-MPRA regulatory region 6253 [ Homo sapiens (human) ]

Gene ID: 125446258, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125446258
Gene description
Sharpr-MPRA regulatory region 6253
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 non-DNase unmatched - State 17:Gen3', transcription 3' end of genes, highly expressed, more exonic) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Jun 2022]
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Genomic context

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See LOC125446258 in Genome Data Viewer
Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (46686312..46686606)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (47174270..47174564)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs1924 Neighboring gene uncharacterized LOC105373075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46947007-46947508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46947509-46948008 Neighboring gene Sharpr-MPRA regulatory region 3871 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46957479-46958230 Neighboring gene Sharpr-MPRA regulatory region 8687 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19242 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:46979179-46980168 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:46980169-46981156 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46982145-46983132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13913 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13914 Neighboring gene GRAM domain containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13915 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46994829-46995328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47014315-47015082 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:47017511-47018022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:47023179-47023964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47026702-47027202 Neighboring gene Sharpr-MPRA regulatory region 10248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47057755-47058338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47065520-47066020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47079427-47079928 Neighboring gene ceramide kinase Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:47106581-47107780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47118736-47119253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47121804-47122304 Neighboring gene uncharacterized LOC105373077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47131961-47132534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47134630-47135288 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:47150047-47150223 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:47157594-47158428 Neighboring gene TBC1D22A 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_081191.1 

    Range
    101..395
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    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
    46686312..46686606
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    47174270..47174564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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