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LOC123881358 Sharpr-MPRA regulatory region 5576 [ Homo sapiens (human) ]

Gene ID: 123881358, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123881358
Gene description
Sharpr-MPRA regulatory region 5576
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 non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 12:CtcfO). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123881358 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (161618837..161619131)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (162977583..162977877)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (162039869..162040163)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901456 Neighboring gene MPRA-validated peak6306 silencer Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:161864752-161865258 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:161865259-161865763 Neighboring gene uncharacterized LOC105378098 Neighboring gene NANOG hESC enhancer GRCh37_chr6:161919346-161919847 Neighboring gene parkin RBR E3 ubiquitin protein ligase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:161939551-161940051 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:161954848-161955039 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:162074308-162074601 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:162074817-162076016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:162103227-162103804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:162102647-162103226 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:162148005-162148758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25415 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:162399319-162399820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:162399821-162400320 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:162484237-162485436 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:162520224-162521423 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:162621359-162622558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:162639333-162639833 Neighboring gene uncharacterized LOC105378097 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:162759597-162760144 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:162760145-162760692 Neighboring gene uncharacterized LOC105369171

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_078263.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    161618837..161619131
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    162977583..162977877
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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