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LOC112272607 Sharpr-MPRA regulatory region 3237 [ Homo sapiens (human) ]

Gene ID: 112272607, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112272607
Gene description
Sharpr-MPRA regulatory region 3237
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 DNase matched - State 9:DNaseU, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 21:Repr, strong Polycomb repression). [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 (68586290..68586584)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (66409184..66409478)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (68878629..68878923)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903513 Neighboring gene uncharacterized LOC105370873 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:68799611-68800181 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68810923-68811424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68811425-68811924 Neighboring gene coronin 2B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68842985-68843486 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68871520-68872387 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68882548-68883339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68892023-68892602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68893807-68894366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68900721-68901361 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68906675-68907190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68933009-68933520 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68933521-68934032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68934266-68934783 Neighboring gene uncharacterized LOC124903514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68943583-68944150 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:68944208-68944708 Neighboring gene Sharpr-MPRA regulatory region 8573 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:68961677-68962176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68966278-68966778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68987247-68987836 Neighboring gene heart enhancer 11 Neighboring gene cysteinyl-tRNA synthetase 1 pseudogene 1

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_056743.1 

    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
    68586290..68586584
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    66409184..66409478
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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