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LOC125146439 Sharpr-MPRA regulatory region 12104 [ Homo sapiens (human) ]

Gene ID: 125146439, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125146439
Gene description
Sharpr-MPRA regulatory region 12104
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 unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125146439 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (29674248..29674542)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29956289..29956583)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene carbonic anhydrase 5A pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10660 Neighboring gene Sharpr-MPRA regulatory region 12377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10661 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7329 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10665 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29688005-29688506 Neighboring gene sialophorin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29688507-29689006 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29690545-29691046 Neighboring gene quinolinate phosphoribosyltransferase Neighboring gene Sharpr-MPRA regulatory region 8247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29706317-29706848 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:29710774-29710948 Neighboring gene CRISPRi-validated cis-regulatory element chr16.2261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7331 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29720469-29721050 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29721051-29721632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29723379-29723960 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29731775-29732277 Neighboring gene RN7SK pseudogene 127

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_080365.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    29674248..29674542
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    29956289..29956583
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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