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LOC125177336 Sharpr-MPRA regulatory region 10086 [ Homo sapiens (human) ]

Gene ID: 125177336, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177336
Gene description
Sharpr-MPRA regulatory region 10086
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177336 in Genome Data Viewer
Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (67459066..67459360)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (73253842..73254136)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene zinc finger DHHC-type containing 1 Neighboring gene uncharacterized LOC124903702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67450269-67450926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67454837-67455408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67458128-67458722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67461918-67462452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67462453-67462987 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67469389-67469890 Neighboring gene hydroxysteroid 11-beta dehydrogenase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67477413-67478036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67478661-67479284 Neighboring gene ATPase H+ transporting V0 subunit d1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67481159-67481658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67485489-67486172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67495532-67496032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67499338-67499838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67499839-67500339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7606 Neighboring gene ATP6V0D1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10967 Neighboring gene agouti related neuropeptide Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10968 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:67548235-67548422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7607 Neighboring gene uncharacterized LOC100505942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10973 Neighboring gene RHO family interacting cell polarization regulator 1

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_080404.1 

    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
    67459066..67459360
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    73253842..73254136
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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