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LOC113939980 Sharpr-MPRA regulatory region 1052 [ Homo sapiens (human) ]

Gene ID: 113939980, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113939980
Gene description
Sharpr-MPRA regulatory region 1052
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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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (166950192..166950486)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (166296022..166296316)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (166919429..166919723)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene transcriptional adaptor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1513 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2027 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:166852951-166853452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:166853453-166853952 Neighboring gene deoxyuridine triphosphatase pseudogene 6 Neighboring gene uncharacterized LOC124904450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:166871233-166871733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2028 Neighboring gene immunoglobulin like domain containing receptor 2 Neighboring gene uncharacterized LOC124904449 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1516 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1518 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:166958090-166959289 Neighboring gene maelstrom spermatogenic transposon silencer Neighboring gene RNA, 5S ribosomal pseudogene 65 Neighboring gene small nucleolar RNA U13

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_063761.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    166950192..166950486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    166296022..166296316
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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