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LOC125446273 Sharpr-MPRA regulatory region 4999 [ Homo sapiens (human) ]

Gene ID: 125446273, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125446273
Gene description
Sharpr-MPRA regulatory region 4999
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 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Jun 2022]
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Genomic context

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See LOC125446273 in Genome Data Viewer
Location:
Xp
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (16733086..16733380)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (16315568..16315862)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (16751209..16751503)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene CTP synthase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:16647850-16648497 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:16648498-16649144 Neighboring gene microRNA 548am Neighboring gene S100 calcium binding protein G Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20678 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29454 Neighboring gene synapse associated protein 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:16789601-16790126 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:16790127-16790652 Neighboring gene RNA, U7 small nuclear 56 pseudogene Neighboring gene uncharacterized LOC124905250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29455 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:16804156-16804888

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_081204.1 

    Range
    101..395
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    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    16733086..16733380
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    16315568..16315862
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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