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LOC121392946 Sharpr-MPRA regulatory region 12960 [ Homo sapiens (human) ]

Gene ID: 121392946, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121392946
Gene description
Sharpr-MPRA regulatory region 12960
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 K562 erythroleukemia cells (group: K562 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, May 2021]
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Genomic context

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See LOC121392946 in Genome Data Viewer
Location:
11q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (119475298..119475592)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (119496837..119497131)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (119346009..119346303)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene USP2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119290361-119290928 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119292628-119293194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119293195-119293760 Neighboring gene Thy-1 cell surface antigen Neighboring gene double homeobox A pseudogene 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119344129-119344629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119347323-119347824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119347825-119348324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119368781-119369640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3981 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:119381879-119382068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119404367-119404896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119417323-119418037 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119430656-119431156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119431157-119431657 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5631 Neighboring gene uncharacterized LOC124902770 Neighboring gene uncharacterized LOC107984398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119456019-119456834 Neighboring gene keratin 8 pseudogene 7

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_074603.1 

    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
    119475298..119475592
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    119496837..119497131
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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