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LOC125371452 Sharpr-MPRA regulatory region 13615 [ Homo sapiens (human) ]

Gene ID: 125371452, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125371452
Gene description
Sharpr-MPRA regulatory region 13615
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 K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125371452 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 (3467771..3468065)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3445932..3446226)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (3467769..3468063)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3189343-3189846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3189847-3190350 Neighboring gene nicalin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9833 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3227850-3228390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3228391-3228930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3229472-3230011 Neighboring gene CUGBP Elav-like family member 5 Neighboring gene MPRA-validated peak3244 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9834 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9835 Neighboring gene uncharacterized LOC105372244 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:3301113-3301307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9836 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9837 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9839 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13733 Neighboring gene skeletal muscle cis-regulatory module in NFIC intron Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3389688-3390265 Neighboring gene nuclear factor I C Neighboring gene Sharpr-MPRA regulatory region 10296 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3434103-3434880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3434881-3435658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3445307-3445848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3462537-3463072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3463073-3463608 Neighboring gene MPRA-validated peak3246 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3465190-3465690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3465691-3466191 Neighboring gene uncharacterized LOC105372246 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3483217-3483755 Neighboring gene small integral membrane protein 24 Neighboring gene small integral membrane protein 44

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_080722.1 

    Range
    101..395
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    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
    3467771..3468065
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    3445932..3446226
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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