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LOC123620114 Sharpr-MPRA regulatory region 875 [ Homo sapiens (human) ]

Gene ID: 123620114, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123620114
Gene description
Sharpr-MPRA regulatory region 875
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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123620114 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (40947970..40948264)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (40776536..40776830)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (40915709..40916003)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24496 Neighboring gene Sharpr-MPRA regulatory region 15012 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:40758342-40759541 Neighboring gene uncharacterized LOC105375053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24497 Neighboring gene uncharacterized LOC101929555 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:40867240-40867751 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:40867752-40868262 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:40885732-40886434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:40886435-40887135 Neighboring gene Sharpr-MPRA regulatory region 12741 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40916844-40917696 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40951247-40951770 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40951771-40952292 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40964711-40965384 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:40965385-40966057 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24499 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17171 Neighboring gene unc-5 family C-terminal like Neighboring gene translocator protein 2

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_078098.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    40947970..40948264
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    40776536..40776830
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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