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LOC125177452 Sharpr-MPRA regulatory region 2970 [ Homo sapiens (human) ]

Gene ID: 125177452, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177452
Gene description
Sharpr-MPRA regulatory region 2970
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177452 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (30394471..30394765)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (31339101..31339395)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene transmembrane and immunoglobulin domain containing 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:28667189-28667899 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:28667900-28668609 Neighboring gene Sharpr-MPRA regulatory region 7119 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:28672567-28673066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11994 Neighboring gene RNA, U6 small nuclear 990, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:28705846-28706773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11997 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:28715045-28715730 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:28732022-28732693 Neighboring gene carboxypeptidase D Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11999 Neighboring gene golgi SNAP receptor complex member 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:28863435-28863984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:28868427-28868928 Neighboring gene arachidonate 12-lipoxygenase pseudogene 1

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

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_080507.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    30394471..30394765
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    31339101..31339395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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