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LOC121530576 Sharpr-MPRA regulatory region 4521 [ Homo sapiens (human) ]

Gene ID: 121530576, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121530576
Gene description
Sharpr-MPRA regulatory region 4521
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [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 (37019888..37020182)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (34825312..34825606)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (37312089..37312383)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:37169875-37170652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:37170653-37171430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:37172643-37173204 Neighboring gene NANOG hESC enhancer GRCh37_chr15:37173676-37174246 Neighboring gene uncharacterized LOC145845 Neighboring gene NANOG hESC enhancer GRCh37_chr15:37190004-37190592 Neighboring gene NANOG hESC enhancer GRCh37_chr15:37190593-37191179 Neighboring gene Meis homeobox 2 Neighboring gene VISTA enhancer hs181 Neighboring gene microRNA 8063 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:37337602-37338196 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:37338197-37338789 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:37386941-37387802 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6294 Neighboring gene uncharacterized LOC124903465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9197 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6296 Neighboring gene NANOG hESC enhancer GRCh37_chr15:37398796-37399337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6297 Neighboring gene VISTA enhancer hs572 Neighboring gene NANOG hESC enhancer GRCh37_chr15:37528451-37528979 Neighboring gene VISTA enhancer hs599 Neighboring gene uncharacterized LOC105370772

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_074774.1 

    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
    37019888..37020182
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    34825312..34825606
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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