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LOC124819403 Sharpr-MPRA regulatory region 6569 [ Homo sapiens (human) ]

Gene ID: 124819403, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124819403
Gene description
Sharpr-MPRA regulatory region 6569
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 unmatched - State 5:Enh, candidate strong enhancer, 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 (113194104..113194398)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (113170727..113171021)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 73 Neighboring gene microRNA 7106 Neighboring gene DEAD-box helicase 54 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7063 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:113623217-113623866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:113623867-113624517 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113624518-113625167 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113629297-113629950 Neighboring gene RBPJ interacting and tubulin associated 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:113639865-113640756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7067 Neighboring gene IQ motif containing D Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7068 Neighboring gene Sharpr-MPRA regulatory region 2606 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24601 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:113669293-113669843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7072 Neighboring gene two pore segment channel 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:113683649-113684312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:113684313-113684976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113689411-113689911 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7073 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24609 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:113705834-113706026 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24611 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24613 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24616 Neighboring gene microRNA 6762

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_079820.1 

    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
    113194104..113194398
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    113170727..113171021
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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