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LOC121847962 Sharpr-MPRA regulatory region 11003 [ Homo sapiens (human) ]

Gene ID: 121847962, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121847962
Gene description
Sharpr-MPRA regulatory region 11003
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 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 DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jul 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 (99863584..99863878)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (97627197..97627491)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (100403789..100404083)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903563 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:100346147-100346518 Neighboring gene RNA, 7SL, cytoplasmic 484, pseudogene Neighboring gene dynamin 1 pseudogene 46 Neighboring gene ubiquitin conjugating enzyme E2 Q2 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100456801-100457665 Neighboring gene Sharpr-MPRA regulatory region 10020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:100515897-100516492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:100516493-100517088 Neighboring gene uncharacterized LOC105371022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:100521898-100522876 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:100523855-100524832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100532449-100532963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100532964-100533477 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:100537785-100538412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100538413-100539040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100539041-100539668 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 17 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100542118-100542966 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:100556815-100558014 Neighboring gene Sharpr-MPRA regulatory region 8829 Neighboring gene RNA, 5S ribosomal pseudogene 402

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_075988.1 

    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
    99863584..99863878
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    97627197..97627491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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