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LOC125177305 Sharpr-MPRA regulatory region 14159 [ Homo sapiens (human) ]

Gene ID: 125177305, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177305
Gene description
Sharpr-MPRA regulatory region 14159
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 non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177305 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 (50208438..50208732)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (56006245..56006539)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900375 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:50186273-50187230 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7475 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10809 Neighboring gene ribosomal protein L10 pseudogene 14 Neighboring gene MPRA-validated peak2589 silencer Neighboring gene terminal nucleotidyltransferase 4B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50217888-50218450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50218451-50219012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10810 Neighboring gene Sharpr-MPRA regulatory region 8986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:50278238-50278950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:50278951-50279662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7478 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:50280376-50281087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50288095-50288594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:50299606-50300199 Neighboring gene adenylate cyclase 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:50305212-50306046 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:50306047-50306881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50317845-50318346 Neighboring gene microRNA 6771 Neighboring gene Sharpr-MPRA regulatory region 2137 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:50347343-50348542 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:50353005-50354204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10815 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10816 Neighboring gene bromodomain containing 7 Neighboring gene small nucleolar RNA U13

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_080373.1 

    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
    50208438..50208732
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    56006245..56006539
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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