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LOC124849260 Sharpr-MPRA regulatory region 8824 [ Homo sapiens (human) ]

Gene ID: 124849260, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124849260
Gene description
Sharpr-MPRA regulatory region 8824
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, Mar 2022]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (121774983..121775277)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (121771651..121771945)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122070465-122071345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7178 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122076353-122076870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122076871-122077388 Neighboring gene ORAI calcium release-activated calcium modulator 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122088979-122089480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122089481-122089980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122101860-122102399 Neighboring gene uncharacterized LOC105370034 Neighboring gene MORN repeat containing 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122109697-122110623 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122124874-122125860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4984 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4986 Neighboring gene transmembrane protein 120B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122165743-122166363 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122194907-122195407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122204395-122204898 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122207988-122208500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122216872-122217390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122217391-122217909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122227166-122227882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122230665-122231496 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122231502-122232042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122232583-122233123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7187 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122235825-122236366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122236367-122236906 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122236907-122237446 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122237447-122237986 Neighboring gene ras homolog family member F, filopodia associated Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7190 Neighboring gene long intergenic non-protein coding RNA 1089 Neighboring gene SET domain containing 1B, histone lysine methyltransferase

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_079838.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    121774983..121775277
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    121771651..121771945
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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