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LOC125371496 Sharpr-MPRA regulatory region 12805 [ Homo sapiens (human) ]

Gene ID: 125371496, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371496
Gene description
Sharpr-MPRA regulatory region 12805
Gene type
biological region
Feature type(s)
regulatory: 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 repressive element 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 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, May 2022]
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Genomic context

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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (19623700..19623994)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19761209..19761503)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19650412-19651074 Neighboring gene Sharpr-MPRA regulatory region 4095 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19656191-19656874 Neighboring gene cartilage intermediate layer protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19662820-19663379 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19671101-19671600 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:19686115-19686616 Neighboring gene PBX homeobox 4 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:19686617-19687116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19690665-19691164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14362 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19703425-19704049 Neighboring gene PHF5A pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10449 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:19722648-19723212 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10450 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10451 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19739417-19740339 Neighboring gene lysophosphatidic acid receptor 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19753343-19754298 Neighboring gene GEM interacting protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10453 Neighboring gene ATPase 13A1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19772231-19772878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14368 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:19773833-19774815

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

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_080797.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    19623700..19623994
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    19761209..19761503
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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