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LOC112543446 Sharpr-MPRA regulatory region 88 [ Homo sapiens (human) ]

Gene ID: 112543446, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112543446
Gene description
Sharpr-MPRA regulatory region 88
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 unmatched - State 1:Tss). [provided by RefSeq, May 2018]
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Genomic context

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See LOC112543446 in Genome Data Viewer
Location:
19p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (12551455..12551749)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (12679875..12680170)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (12662269..12662563)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene MT-ATP6 pseudogene 27 Neighboring gene peptidylprolyl isomerase A pseudogene 20 Neighboring gene Sharpr-MPRA regulatory region 13330 Neighboring gene zinc finger protein 564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:12660933-12661435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:12663347-12663848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:12663849-12664348 Neighboring gene long intergenic non-protein coding RNA 2926 Neighboring gene phosphoglycerate kinase 1, pseudogene 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:12690738-12691937 Neighboring gene zinc finger protein 490 Neighboring gene vomeronasal 2 receptor 16 pseudogene

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_057395.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    12551455..12551749
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    12679875..12680170
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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