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LOC125177365 Sharpr-MPRA regulatory region 4738 [ Homo sapiens (human) ]

Gene ID: 125177365, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177365
Gene description
Sharpr-MPRA regulatory region 4738
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 5:Enh, candidate strong enhancer, open chromatin). [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 (84541063..84541357)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90607359..90607653)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903736 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84538296-84539243 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7783 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:84540344-84540580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84540853-84541353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84543104-84543903 Neighboring gene uncharacterized LOC124903735 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11237 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84547599-84548206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84557586-84558169 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84558170-84558754 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:84565033-84565246 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84565360-84566037 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:84566038-84566716 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:84566717-84567393 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84577753-84578254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84578255-84578754 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84580244-84580995 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84580996-84581746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84582498-84583247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84589034-84589534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84593245-84593762 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84594827-84595594 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84595595-84596362 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84605929-84606461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11242 Neighboring gene coactosin like F-actin binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84617304-84617809 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84623933-84624432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84631141-84631642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84631643-84632142 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84632885-84633706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84637045-84637609 Neighboring gene Sharpr-MPRA regulatory region 4329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11249 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84647291-84647792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84647793-84648292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84674539-84675097 Neighboring gene uncharacterized LOC105371376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7787 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7788 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7789 Neighboring gene kelch like family member 36

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_080433.1 

    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
    84541063..84541357
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    90607359..90607653
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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