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LOC123956168 Sharpr-MPRA regulatory region 3792 [ Homo sapiens (human) ]

Gene ID: 123956168, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956168
Gene description
Sharpr-MPRA regulatory region 3792
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 DNase matched - State 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956168 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 (75991031..75991325)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (77278598..77278892)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (75620349..75620643)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26184 Neighboring gene RPL7L1 pseudogene 3 Neighboring gene cytochrome p450 oxidoreductase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75563905-75564733 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75566331-75566944 Neighboring gene small nucleolar RNA, H/ACA box 14A Neighboring gene Sharpr-MPRA regulatory region 2709 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:75596037-75596916 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:75612087-75613286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26185 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26187 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18303 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18304 Neighboring gene transmembrane protein 120A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:75630123-75630623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26188 Neighboring gene serine/threonine/tyrosine interacting like 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:75648513-75649014 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75676791-75677573 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75677574-75678355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26192 Neighboring gene malate dehydrogenase 2

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_078362.1 

    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
    75991031..75991325
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    77278598..77278892
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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