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LOC125078045 Sharpr-MPRA regulatory region 9919 [ Homo sapiens (human) ]

Gene ID: 125078045, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125078045
Gene description
Sharpr-MPRA regulatory region 9919
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 HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125078045 in Genome Data Viewer
Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (105498812..105499106)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (99748176..99748470)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105939600-105940132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6239 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6242 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6243 Neighboring gene cysteine rich protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105947154-105947875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9149 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6248 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105954409-105954980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6250 Neighboring gene hESC enhancers GRCh37_chr14:105956919-105957662 and GRCh37_chr14:105957663-105958406 Neighboring gene cysteine rich protein 1 Neighboring gene tubulin epsilon and delta complex 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105974095-105974596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105974597-105975096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105978261-105978760 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:105986957-105987132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6253 Neighboring gene transmembrane protein 121 Neighboring gene uncharacterized LOC105370697

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_080180.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    105498812..105499106
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    99748176..99748470
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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