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LOC123924906 Sharpr-MPRA regulatory region 12730 [ Homo sapiens (human) ]

Gene ID: 123924906, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123924906
Gene description
Sharpr-MPRA regulatory region 12730
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123924906 in Genome Data Viewer
Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (12930724..12931018)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (13061974..13062268)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (12970349..12970643)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 228 Neighboring gene Sharpr-MPRA regulatory region 14677 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:12963056-12964255 Neighboring gene uncharacterized LOC105375158 Neighboring gene Sharpr-MPRA regulatory region 6845 Neighboring gene RBMX2 pseudogene 4 Neighboring gene MPRA-validated peak6391 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:13056242-13057441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25666 Neighboring gene MPRA-validated peak6392 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr7:13279910-13280411 Neighboring gene uncharacterized LOC107986770 Neighboring gene NANOG hESC enhancer GRCh37_chr7:13346662-13347177 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:13361588-13362292 Neighboring gene VISTA enhancer hs749 Neighboring gene VISTA enhancer hs550 Neighboring gene MPRA-validated peak6396 silencer Neighboring gene MPRA-validated peak6397 silencer

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_078298.1 

    Range
    101..395
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    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    12930724..12931018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    13061974..13062268
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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