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LOC125371542 Sharpr-MPRA regulatory region 2382 [ Homo sapiens (human) ]

Gene ID: 125371542, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125371542
Gene description
Sharpr-MPRA regulatory region 2382
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 non-DNase unmatched - 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 LOC125371542 in Genome Data Viewer
Location:
19q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (48627332..48627626)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (51621812..51622106)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (49130589..49130883)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 83 member E Neighboring gene sperm acrosome associated 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:49117268-49117444 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49117749-49118580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49118581-49119412 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49119413-49120243 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:49121076-49121906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14903 Neighboring gene ribosomal protein L18 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10889 Neighboring gene sphingosine kinase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49130943-49131443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10890 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10893 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14904 Neighboring gene D-box binding PAR bZIP transcription factor Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:49147372-49148073 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49148074-49148774 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49148775-49149475 Neighboring gene secretory blood group 1, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10896 Neighboring gene carbonic anhydrase 11

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 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_080843.1 

    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
    48627332..48627626
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    51621812..51622106
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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