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LOC123575680 Sharpr-MPRA regulatory region 4383 [ Homo sapiens (human) ]

Gene ID: 123575680, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575680
Gene description
Sharpr-MPRA regulatory region 4383
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 19:H4K20, transcription, primarily H4K20me1, more intronic). [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 (15308818..15309112)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (15182025..15182319)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (15309049..15309343)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15244415-15244928 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16949 Neighboring gene nonconserved acetylation island sequence 83 enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15251871-15252646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24066 Neighboring gene JARID2 divergent transcript Neighboring gene JARID2 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:15264949-15265458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24067 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15267598-15268156 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15268157-15268714 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:15268715-15269273 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:15269274-15269831 Neighboring gene jumonji and AT-rich interaction domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15280804-15281784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24069 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15291865-15292366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24074 Neighboring gene RNA, U6 small nuclear 522, pseudogene Neighboring gene RNA, U6 small nuclear 645, pseudogene

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_077939.1 

    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
    15308818..15309112
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    15182025..15182319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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