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LOC125177341 Sharpr-MPRA regulatory region 7703 [ Homo sapiens (human) ]

Gene ID: 125177341, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177341
Gene description
Sharpr-MPRA regulatory region 7703
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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177341 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 (68297986..68298280)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (74093768..74094062)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903704 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7645 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:68298967-68300166 Neighboring gene solute carrier family 7 member 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11009 Neighboring gene Sharpr-MPRA regulatory region 10574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11010 Neighboring gene Sharpr-MPRA regulatory region 6227 Neighboring gene RNA, U6 small nuclear 1262, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11012 Neighboring gene solute carrier family 7 member 6 opposite strand Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:68343854-68344818 Neighboring gene small nucleolar RNA U13 Neighboring gene protein arginine methyltransferase 7 Neighboring gene RNA, U4 small nuclear 30, pseudogene

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_080409.1 

    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
    68297986..68298280
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    74093768..74094062
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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