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LOC123620092 Sharpr-MPRA regulatory region 11676 [ Homo sapiens (human) ]

Gene ID: 123620092, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123620092
Gene description
Sharpr-MPRA regulatory region 11676
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Dec 2021]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (34514532..34514826)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (34338381..34338675)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (34482309..34482603)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RPS10-NUDT3 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24380 Neighboring gene nudix hydrolase 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:34292259-34292900 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:34294990-34295799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34322011-34322510 Neighboring gene Sharpr-MPRA regulatory region 13549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17073 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17074 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17075 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34393285-34393989 Neighboring gene ribosomal protein S10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17077 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34440734-34441492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24383 Neighboring gene protein kinase C and casein kinase substrate in neurons 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34457197-34457701 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34481139-34482042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34484751-34485653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17079 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34495675-34496656 Neighboring gene Sharpr-MPRA regulatory region 1455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34502315-34502814 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:34505376-34505582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34518352-34519346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34522694-34523210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34528110-34528841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34528842-34529572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34529573-34530303 Neighboring gene SAM pointed domain containing ETS transcription factor Neighboring gene IFITM3 pseudogene 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_078076.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    34514532..34514826
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    34338381..34338675
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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