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LOC123956158 Sharpr-MPRA regulatory region 8911 [ Homo sapiens (human) ]

Gene ID: 123956158, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956158
Gene description
Sharpr-MPRA regulatory region 8911
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956158 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 (69732263..69732557)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (70955040..70955334)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (69197249..69197543)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26093 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18224 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:69073614-69074587 Neighboring gene NANOG hESC enhancer GRCh37_chr7:69075092-69075654 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26096 Neighboring gene Sharpr-MPRA regulatory region 1350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26100 Neighboring gene activator of transcription and developmental regulator AUTS2 Neighboring gene cancer/testis associated transcript 66 Neighboring gene NANOG hESC enhancer GRCh37_chr7:69209815-69210316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26103 Neighboring gene VISTA enhancer hs2315 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26104 Neighboring gene VISTA enhancer hs1660 Neighboring gene NANOG hESC enhancer GRCh37_chr7:69537097-69537598 Neighboring gene VISTA enhancer hs1425 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:69604114-69604315 Neighboring gene NANOG hESC enhancer GRCh37_chr7:69615911-69616412 Neighboring gene VISTA enhancer hs2316 Neighboring gene heart enhancer 21 Neighboring gene VISTA enhancer hs658 Neighboring gene VISTA enhancer hs2317 Neighboring gene VISTA enhancer hs2318 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:69813727-69814226 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:69857943-69858138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26109 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:69881219-69881824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:69881825-69882428 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:69917332-69917455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:69961601-69962108 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:69969942-69971141 Neighboring gene uncharacterized LOC124901669 Neighboring gene uncharacterized LOC124901668

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_078352.1 

    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
    69732263..69732557
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    70955040..70955334
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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