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LOC113875032 Sharpr-MPRA regulatory region 2669 [ Homo sapiens (human) ]

Gene ID: 113875032, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113875032
Gene description
Sharpr-MPRA regulatory region 2669
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer 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 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Dec 2018]
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Genomic context

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Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (49039844..49040138)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (48451447..48451741)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (48897369..48897663)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 12141 Neighboring gene potassium voltage-gated channel subfamily D member 1 Neighboring gene GRIP1 associated protein 1 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:48840212-48840468 Neighboring gene Sharpr-MPRA regulatory region 9113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29627 Neighboring gene CRISPRi-FlowFISH-validated HDAC6 regulatory element 4 Neighboring gene transcription factor binding to IGHM enhancer 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:48900209-48901072 Neighboring gene CRISPRi-FlowFISH-validated PQBP1 regulatory element 4 Neighboring gene Sharpr-MPRA regulatory region 13918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20833 Neighboring gene coiled-coil domain containing 120 Neighboring gene PRA1 domain family member 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_063220.1 

    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    49039844..49040138
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791820.1 Reference GRCh38.p14 PATCHES

    Range
    198679..198973
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    48451447..48451741
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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