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LOC121392909 Sharpr-MPRA regulatory region 15340 [ Homo sapiens (human) ]

Gene ID: 121392909, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121392909
Gene description
Sharpr-MPRA regulatory region 15340
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 unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 12:CtcfO). [provided by RefSeq, May 2021]
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Genomic context

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See LOC121392909 in Genome Data Viewer
Location:
11p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (45110638..45110932)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (45268158..45268452)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (45132189..45132483)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376649 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44996027-44996672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44997901-44998858 Neighboring gene long intergenic non-protein coding RNA 2685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45011181-45012070 Neighboring gene uncharacterized LOC105376650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45062883-45063384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45070929-45071428 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:45072318-45072505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45096169-45096784 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:45096785-45097399 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3283 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45103805-45104682 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45104683-45105558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45108817-45109553 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:45122734-45123274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45123275-45123813 Neighboring gene Sharpr-MPRA regulatory region 3485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3284 Neighboring gene uncharacterized LOC105376652 Neighboring gene PR/SET domain 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45149168-45149668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45149669-45150169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45203073-45203804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45230951-45231698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45231699-45232446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45232447-45233193 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45233771-45234633 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45234634-45235495 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45240557-45241118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45241119-45241678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45265182-45265682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45288476-45288976 Neighboring gene synaptotagmin 13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45307287-45308073 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:45320242-45320786 Neighboring gene Sharpr-MPRA regulatory region 11350 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:45368824-45369362 Neighboring gene long intergenic non-protein coding RNA 2696

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_074566.1 

    Range
    101..395
    Download
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    45110638..45110932
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    45268158..45268452
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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