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LOC113939944 Sharpr-MPRA regulatory region 9539 [ Homo sapiens (human) ]

Gene ID: 113939944, updated on 17-Sep-2024

Summary

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Gene symbol
LOC113939944
Gene description
Sharpr-MPRA regulatory region 9539
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Jan 2019]
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Genomic context

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See LOC113939944 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 (48520532..48520826)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (46328738..46329032)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (48812729..48813023)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903486 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:48621665-48621855 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:48623134-48623660 Neighboring gene Sharpr-MPRA regulatory region 3998 Neighboring gene DUT antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6416 Neighboring gene deoxyuridine triphosphatase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:48707937-48708437 Neighboring gene fibrillin 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:48764566-48765765 Neighboring gene Sharpr-MPRA regulatory region 3576 Neighboring gene uncharacterized LOC124903488 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:48821930-48823129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6417 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6419 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:48937944-48938468 Neighboring gene FBN1 divergent transcript

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 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_063729.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    48520532..48520826
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    46328738..46329032
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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