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LOC113939943 Sharpr-MPRA regulatory region 12620 [ Homo sapiens (human) ]

Gene ID: 113939943, updated on 17-Sep-2024

Summary

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Gene symbol
LOC113939943
Gene description
Sharpr-MPRA regulatory region 12620
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 2019]
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Genomic context

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See LOC113939943 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (34648328..34648622)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (32453732..32454026)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (34940529..34940823)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene golgin A8 family member B Neighboring gene amyloid beta precursor protein binding family A member 2 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:34861909-34862858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6289 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6290 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:34876125-34876626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:34876627-34877127 Neighboring gene MPRA-validated peak2294 silencer Neighboring gene Sharpr-MPRA regulatory region 9988 Neighboring gene uncharacterized LOC124903462 Neighboring gene long intergenic non-protein coding RNA 2252 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:34974212-34975411 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:35013869-35014370 Neighboring gene uncharacterized LOC124903463

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_063728.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    34648328..34648622
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    32453732..32454026
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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