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LOC123956234 Sharpr-MPRA regulatory region 13047 [ Homo sapiens (human) ]

Gene ID: 123956234, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956234
Gene description
Sharpr-MPRA regulatory region 13047
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 DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956234 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 (137862383..137862677)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (139171478..139171772)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (137547129..137547423)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375527 Neighboring gene pleiotrophin Neighboring gene pleiotrophin promoter Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:137124520-137125036 Neighboring gene diacylglycerol kinase iota Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:137177340-137177840 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:137275182-137275682 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:137275817-137277016 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:137327058-137327746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26725 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:137431381-137432117 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:137438995-137439495 Neighboring gene ribosomal protein L6 pseudogene 19 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:137467087-137467587 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:137504722-137505502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26726 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:137524999-137525581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:137530559-137531060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18684 Neighboring gene Sharpr-MPRA regulatory region 15617 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:137558107-137559306 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr7:137563379-137564110 and GRCh37_chr7:137564111-137564844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:137568315-137568816 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:137569503-137570060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26728 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:137584118-137584834 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:137588782-137589282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26730 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:137616267-137616482 Neighboring gene cAMP responsive element binding protein 3 like 2 Neighboring gene Sharpr-MPRA regulatory region 2088 Neighboring gene CREB3L2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:137662984-137663912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26731 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26735 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26736 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:137685857-137686455 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:137686456-137687053 Neighboring gene uncharacterized LOC124901752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26740

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_078428.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    137862383..137862677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    139171478..139171772
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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