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LOC123956246 Sharpr-MPRA regulatory region 12519 [ Homo sapiens (human) ]

Gene ID: 123956246, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956246
Gene description
Sharpr-MPRA regulatory region 12519
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956246 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (139888090..139888384)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (141201296..141201590)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (139587889..139588183)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375530 Neighboring gene homeodomain interacting protein kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26765 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:139311135-139311345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18698 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:139365244-139366443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26767 Neighboring gene NANOG hESC enhancer GRCh37_chr7:139377579-139378080 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:139411674-139412500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139416415-139416915 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139415914-139416414 Neighboring gene Sharpr-MPRA regulatory region 6205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18700 Neighboring gene Sharpr-MPRA regulatory region 3006 Neighboring gene MPRA-validated peak6784 silencer Neighboring gene thromboxane A synthase 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:139528736-139529935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26770 Neighboring gene uncharacterized LOC107986853 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:139613504-139614703 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:139615605-139616804 Neighboring gene uncharacterized LOC105375532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139637955-139638455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139655263-139655763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139656695-139657195 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139687657-139688158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139688714-139689231 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139688159-139688658 Neighboring gene MPRA-validated peak6785 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139716538-139717038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18701 Neighboring gene MPRA-validated peak6786 silencer Neighboring gene MPRA-validated peak6788 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26773 Neighboring gene poly(ADP-ribose) polymerase family member 12

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_078440.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    139888090..139888384
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    141201296..141201590
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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