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LOC121838576 Sharpr-MPRA regulatory region 10224 [ Homo sapiens (human) ]

Gene ID: 121838576, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121838576
Gene description
Sharpr-MPRA regulatory region 10224
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer 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 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
13q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (52087833..52088127)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (51302665..51302959)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (52661969..52662263)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ATPase copper transporting beta Neighboring gene fatty acid binding protein 5 pseudogene 2 Neighboring gene Sharpr-MPRA regulatory region 15635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5379 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7786 Neighboring gene ALG11 alpha-1,2-mannosyltransferase Neighboring gene UTP14C small subunit processome component Neighboring gene NIMA related kinase 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:52653033-52653791 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:52653792-52654549 Neighboring gene Sharpr-MPRA regulatory region 2352 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:52696487-52696693 Neighboring gene uncharacterized LOC101929657 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:52706487-52707686 Neighboring gene uncharacterized LOC124903176 Neighboring gene NIMA related kinase 3

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

See Variation Viewer (GRCh37.p13)

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_075939.1 

    Range
    101..395
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    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
    52087833..52088127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    51302665..51302959
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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