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LOC123620108 Sharpr-MPRA regulatory region 1536 [ Homo sapiens (human) ]

Gene ID: 123620108, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123620108
Gene description
Sharpr-MPRA regulatory region 1536
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with 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 (38012593..38012887)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (37837338..37837632)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (37980369..37980663)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 285, pseudogene Neighboring gene MPRA-validated peak5795 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24481 Neighboring gene MPRA-validated peak5796 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:37849025-37849590 Neighboring gene zinc finger AN1-type containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17158 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37896413-37896914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17160 Neighboring gene RNA, variant U1 small nuclear 33 Neighboring gene NANOG hESC enhancer GRCh37_chr6:38087202-38088004 Neighboring gene uncharacterized LOC124901314 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:38105943-38106787 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:38120813-38121433 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:38129468-38130436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:38135966-38136596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:38136597-38137228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:38137229-38137860 Neighboring gene uncharacterized LOC124901315 Neighboring gene BTB domain containing 9

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_078092.1 

    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
    38012593..38012887
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    37837338..37837632
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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