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LOC125078081 Sharpr-MPRA regulatory region 7002 [ Homo sapiens (human) ]

Gene ID: 125078081, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125078081
Gene description
Sharpr-MPRA regulatory region 7002
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (52011792..52012086)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (49820537..49820831)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268148 Neighboring gene LEO1 homolog, Paf1/RNA polymerase II complex component pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9409 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:52239187-52239400 Neighboring gene LEO1 homolog, Paf1/RNA polymerase II complex component Neighboring gene H3K27ac hESC enhancers GRCh37_chr15:52263092-52263668 and GRCh37_chr15:52263669-52264244 Neighboring gene mitogen-activated protein kinase 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9412 Neighboring gene Sharpr-MPRA regulatory region 2333 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9415 Neighboring gene MAPK6 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:52317121-52317701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9416 Neighboring gene MPRA-validated peak2339 silencer Neighboring gene uncharacterized LOC112268150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9417 Neighboring gene uncharacterized LOC124903494 Neighboring gene MAPK6-RPS13P8 intergenic CAGE-defined mid-level expression enhancer Neighboring gene ReSE screen-validated silencer GRCh37_chr15:52386957-52387157 Neighboring gene ribosomal protein S13 pseudogene 8

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_080217.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    52011792..52012086
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    49820537..49820831
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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