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LOC123864087 Sharpr-MPRA regulatory region 15423 [ Homo sapiens (human) ]

Gene ID: 123864087, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123864087
Gene description
Sharpr-MPRA regulatory region 15423
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 unmatched - State 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123864087 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (142207452..142207746)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (143399490..143399784)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (142528589..142528883)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986654 Neighboring gene MPRA-validated peak6171 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:142409105-142409658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:142409659-142410210 Neighboring gene neuromedin B receptor Neighboring gene Sharpr-MPRA regulatory region 1984 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:142468581-142469101 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:142476776-142477403 Neighboring gene gap junction protein epsilon 1 Neighboring gene vesicle trafficking 1 Neighboring gene long intergenic non-protein coding RNA 2919 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:142596514-142597713 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17614 Neighboring gene Sharpr-MPRA regulatory region 14737 Neighboring gene adhesion G protein-coupled receptor G6 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:142695388-142695989 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:142695947-142697146 Neighboring gene Sharpr-MPRA regulatory regions 3748 and 6738

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

See Variation Viewer (GRCh37.p13)

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_078219.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    142207452..142207746
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    143399490..143399784
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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