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LOC123864095 Sharpr-MPRA regulatory region 3301 [ Homo sapiens (human) ]

Gene ID: 123864095, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123864095
Gene description
Sharpr-MPRA regulatory region 3301
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 DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123864095 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (145600313..145600607)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (146793384..146793678)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (145921449..145921743)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene EPM2A glucan phosphatase, laforin Neighboring gene RNA, U1 small nuclear 33, pseudogene Neighboring gene zinc finger protein 131 pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:145851539-145852203 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:145852204-145852867 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:145852881-145853456 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:145853457-145854032 Neighboring gene NANOG hESC enhancer GRCh37_chr6:145874002-145874503 Neighboring gene Sharpr-MPRA regulatory region 9117 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:145994233-145994904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:145994905-145995576 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25226 Neighboring gene uncharacterized LOC105378039 Neighboring gene EPM2A divergent transcript Neighboring gene uncharacterized LOC124901419

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_078227.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    145600313..145600607
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    146793384..146793678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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