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LOC125177363 Sharpr-MPRA regulatory region 13657 [ Homo sapiens (human) ]

Gene ID: 125177363, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177363
Gene description
Sharpr-MPRA regulatory region 13657
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 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (83974164..83974458)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90040220..90040514)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene malonyl-CoA decarboxylase Neighboring gene uncharacterized LOC105371372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83987658-83988427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7772 Neighboring gene oxidative stress induced growth inhibitor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84007063-84007564 Neighboring gene N-terminal EF-hand calcium binding protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7773 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84035929-84036711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84050003-84050504 Neighboring gene solute carrier family 38 member 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84060729-84061230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84066580-84067080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84075154-84075858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84075859-84076562 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:84076563-84077267 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:84077268-84077971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84078959-84079731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84082148-84083032 Neighboring gene RNA, 5S ribosomal pseudogene 432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84088845-84089438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84089439-84090031 Neighboring gene membrane bound transcription factor peptidase, site 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7775 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:84125154-84126353 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7776

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_080431.1 

    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
    83974164..83974458
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    90040220..90040514
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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