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LOC124946347 Sharpr-MPRA regulatory region 1096 [ Homo sapiens (human) ]

Gene ID: 124946347, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124946347
Gene description
Sharpr-MPRA regulatory region 1096
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC124946347 in Genome Data Viewer
Location:
13q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (114226774..114227068)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (113435434..113435728)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (114992249..114992543)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene RAS p21 protein activator 3 Neighboring gene uncharacterized LOC107987192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114892696-114893197 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114895306-114895935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8056 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114897194-114897821 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114900119-114900619 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114906114-114907109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8058 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114916272-114916772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114916773-114917273 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114927227-114928127 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114951001-114951592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114952186-114952777 Neighboring gene CFAP97 domain containing 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:114993807-114994308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5558 Neighboring gene uncharacterized LOC105370384 Neighboring gene microRNA 548ar Neighboring gene cell division cycle 16 Neighboring gene microRNA 4502

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 8060

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_080053.1 

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    114226774..114227068
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    113435434..113435728
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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