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LOC121530587 Sharpr-MPRA regulatory region 12968 [ Homo sapiens (human) ]

Gene ID: 121530587, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121530587
Gene description
Sharpr-MPRA regulatory region 12968
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer 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 Activating non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, May 2021]
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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 (67414131..67414425)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (65236123..65236417)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (67706469..67706763)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene SMAD family member 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67438421-67439356 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67439357-67440291 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67440670-67441477 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:67442285-67443092 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40599 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40600 Neighboring gene SMAD3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67459191-67459860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67459861-67460532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:67460533-67461202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9625 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9627 Neighboring gene alpha and gamma adaptin binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9628 Neighboring gene ribosomal protein S24 pseudogene 16 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:67569773-67569933 Neighboring gene IQ motif containing H Neighboring gene VISTA enhancer hs358 Neighboring gene IQCH antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 13361 Neighboring gene uncharacterized LOC124903511 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:67794233-67794407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9630 Neighboring gene chromosome 15 open reading frame 61

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_074785.1 

    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
    67414131..67414425
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    65236123..65236417
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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