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LOC113960609 Sharpr-MPRA regulatory region 13448 [ Homo sapiens (human) ]

Gene ID: 113960609, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113960609
Gene description
Sharpr-MPRA regulatory region 13448
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 DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 12:CtcfO). [provided by RefSeq, Jan 2019]
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Genomic context

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See LOC113960609 in Genome Data Viewer
Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (44248169..44248463)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (45982834..45983128)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (42876809..42877103)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene junctophilin 2 Neighboring gene uncharacterized LOC124904909 Neighboring gene JPH2 intron CAGE-defined T cell enhancer Neighboring gene ReSE screen-validated silencer GRCh37_chr20:42795218-42795478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42806021-42806521 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:42809003-42809909 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42810816-42811722 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:42832370-42833569 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42838821-42839440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12940 Neighboring gene oxidative stress responsive serine rich 1 Neighboring gene OSER1 divergent transcript Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42860439-42861068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42875650-42876448 Neighboring gene ganglioside induced differentiation associated protein 1 like 1 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:42900885-42901394 Neighboring gene Sharpr-MPRA regulatory region 2613 Neighboring gene uncharacterized LOC124904910 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42938689-42939418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42939419-42940148 Neighboring gene fat storage inducing transmembrane 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_063772.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    44248169..44248463
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    45982834..45983128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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