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LOC123956222 Sharpr-MPRA regulatory region 12451 [ Homo sapiens (human) ]

Gene ID: 123956222, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123956222
Gene description
Sharpr-MPRA regulatory region 12451
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 3:PromF, promoter flanking). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956222 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (130203889..130204183)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (131517279..131517573)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (129843729..129844023)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129781469-129782132 Neighboring gene long intergenic non-protein coding RNA 3008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18643 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18644 Neighboring gene transmembrane protein 209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26649 Neighboring gene uncharacterized LOC124901745 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129844685-129845484 Neighboring gene serine rich single-pass membrane protein 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129912168-129912820 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129912821-129913472 Neighboring gene Sharpr-MPRA regulatory region 5425 Neighboring gene carboxypeptidase A2

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_078416.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    130203889..130204183
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    131517279..131517573
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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