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LOC125078089 Sharpr-MPRA regulatory region 13950 [ Homo sapiens (human) ]

Gene ID: 125078089, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125078089
Gene description
Sharpr-MPRA regulatory region 13950
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 non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125078089 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (60006610..60006904)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (57808296..57808590)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (60298809..60299103)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene DEAD-box helicase 18 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9501 Neighboring gene NMNAT1 pseudogene 5 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:60287460-60288247 Neighboring gene NANOG hESC enhancer GRCh37_chr15:60296191-60296706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9503 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:60301179-60301777 Neighboring gene forkhead box B1 Neighboring gene uncharacterized LOC105370838 Neighboring gene mesoderm specific transcript pseudogene 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 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_080225.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    60006610..60006904
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    57808296..57808590
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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