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LOC123775400 Sharpr-MPRA regulatory region 15105 [ Homo sapiens (human) ]

Gene ID: 123775400, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123775400
Gene description
Sharpr-MPRA regulatory region 15105
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123775400 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 (108707366..108707660)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (109884723..109885017)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (109028569..109028863)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17453 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17454 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:108882597-108883097 Neighboring gene Sharpr-MPRA regulatory region 14072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24915 Neighboring gene forkhead box O3 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:108908380-108908581 Neighboring gene SUMO2 pseudogene 8 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:108960200-108960701 Neighboring gene Sharpr-MPRA regulatory region 11562 Neighboring gene MPRA-validated peak6015 silencer Neighboring gene Sharpr-MPRA regulatory region 11560 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:109019778-109020977 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:109051727-109052654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109052989-109053781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109053782-109054573 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:109057555-109058224 Neighboring gene uncharacterized LOC107986629 Neighboring gene long intergenic non-protein coding RNA 222

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_078169.1 

    Range
    101..395
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    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
    108707366..108707660
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    109884723..109885017
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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