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LOC123956188 Sharpr-MPRA regulatory region 11703 [ Homo sapiens (human) ]

Gene ID: 123956188, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956188
Gene description
Sharpr-MPRA regulatory region 11703
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 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (100486326..100486620)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (101726402..101726696)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (100083949..100084243)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene TSC22D4-C7orf61 readthrough Neighboring gene ReSE screen-validated silencer GRCh37_chr7:100054725-100054887 Neighboring gene sperm acrosome developmental regulator Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18436 Neighboring gene TSC22 domain family member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100069322-100070108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100070109-100070893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26368 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26369 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:100080938-100081153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18439 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100081845-100082371 Neighboring gene Sharpr-MPRA regulatory region 1011 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100087809-100088334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100088335-100088858 Neighboring gene neuronal tyrosine phosphorylated phosphoinositide-3-kinase adaptor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18440 Neighboring gene uncharacterized LOC107986829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26370 Neighboring gene RNA, 7SL, cytoplasmic 416, 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_078382.1 

    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
    100486326..100486620
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    101726402..101726696
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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