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LOC124849274 Sharpr-MPRA regulatory region 13038 [ Homo sapiens (human) ]

Gene ID: 124849274, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124849274
Gene description
Sharpr-MPRA regulatory region 13038
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 21:Repr, strong Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [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 (124190383..124190677)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (124192170..124192464)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene dynein axonemal heavy chain 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124422596-124423096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124423097-124423597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124438925-124439426 Neighboring gene NANOG hESC enhancer GRCh37_chr12:124453330-124453831 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124456125-124456862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5053 Neighboring gene ZNF664-RFLNA readthrough Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124456863-124457600 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5056 Neighboring gene coiled-coil domain containing 92 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7279 Neighboring gene zinc finger protein 664 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:124556312-124557118 Neighboring gene NANOG hESC enhancer GRCh37_chr12:124594949-124595450 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124600014-124600560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124601106-124601651 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124601652-124602196 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:124608857-124609358 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:124624781-124625523 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124625524-124626265 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:124630091-124630857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124666563-124667068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124672143-124672663 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124672664-124673183 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124673184-124673704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124725860-124726762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124786919-124787420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124801665-124802264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7283 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:124821000-124821180 Neighboring gene refilin A Neighboring gene microRNA 6880 Neighboring gene nuclear receptor corepressor 2

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_079849.1 

    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
    124190383..124190677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    124192170..124192464
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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