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LOC124629417 Sharpr-MPRA regulatory region 15641 [ Homo sapiens (human) ]

Gene ID: 124629417, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124629417
Gene description
Sharpr-MPRA regulatory region 15641
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 non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124629417 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (77678469..77678763)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (77656398..77656692)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:77631785-77632286 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:77633489-77633990 Neighboring gene long intergenic non-protein coding RNA 2464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4678 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:77741435-77742634 Neighboring gene uncharacterized LOC124902972 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:78038694-78039502 Neighboring gene NANOG hESC enhancer GRCh37_chr12:78039827-78040389 Neighboring gene Sharpr-MPRA regulatory region 9790 Neighboring gene neuron navigator 3 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:78282205-78283404 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:78333298-78334497 Neighboring gene NANOG hESC enhancer GRCh37_chr12:78375957-78376518 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:78495967-78496468 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:78496469-78496968 Neighboring gene peroxiredoxin like 2A pseudogene 1 Neighboring gene uncharacterized LOC105369859 Neighboring gene long intergenic non-protein coding RNA 2424

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_079776.1 

    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
    77678469..77678763
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    77656398..77656692
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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