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LOC125371486 Sharpr-MPRA regulatory region 12980 [ Homo sapiens (human) ]

Gene ID: 125371486, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371486
Gene description
Sharpr-MPRA regulatory region 12980
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 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 (15864879..15865173)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (15993113..15993407)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 861, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:15939001-15940200 Neighboring gene collagen alpha-1(I) chain-like Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:15945748-15946947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14193 Neighboring gene urothelial cancer associated 1 Neighboring gene C-type lectin domain family 4 member O, pseudogene Neighboring gene cytochrome P450 family 4 subfamily F member 36, pseudogene Neighboring gene cytochrome P450 family 4 subfamily F member 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:16002896-16004095

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_080756.1 

    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
    15864879..15865173
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    15993113..15993407
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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