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LOC121366068 Sharpr-MPRA regulatory region 13339 [ Homo sapiens (human) ]

Gene ID: 121366068, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121366068
Gene description
Sharpr-MPRA regulatory region 13339
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, May 2021]
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Genomic context

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Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (84352273..84352567)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (85230764..85231059)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (86112029..86112323)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:86004955-86005454 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2553 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:86028972-86030171 Neighboring gene retinal G protein coupled receptor Neighboring gene long intergenic non-protein coding RNA 858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:86057631-86058131 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:86073792-86074670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3681 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17641 Neighboring gene coiled-coil serine rich protein 2 Neighboring gene ribosomal protein L12 pseudogene 29 Neighboring gene transportin 1 pseudogene 1

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_074418.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    84352273..84352567
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    85230764..85231059
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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