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LOC124946344 Sharpr-MPRA regulatory region 10208 [ Homo sapiens (human) ]

Gene ID: 124946344, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124946344
Gene description
Sharpr-MPRA regulatory region 10208
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 Sharpr-MPRA (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). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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 LOC124946344 in Genome Data Viewer
Location:
13q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (113299954..113300248)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (112553622..112553916)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene cullin 4A Neighboring gene microRNA 8075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113928297-113928796 Neighboring gene Sharpr-MPRA regulatory region 2925 Neighboring gene lactate dehydrogenase B pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113945996-113946505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113946506-113947014 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8037 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:113959050-113959215 Neighboring gene lysosomal associated membrane protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113967994-113968742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113968743-113969490 Neighboring gene growth hormone regulated TBC protein 1 Neighboring gene MAGE-like protein 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:114003074-114003239 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114003888-114004548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114004549-114005209 Neighboring gene GRTP1 antisense RNA 1

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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 variants in ClinVar

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 5544

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_080050.1 

    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    113299954..113300248
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    112553622..112553916
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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