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LOC112081399 Sharpr-MPRA regulatory region 12058 [ Homo sapiens (human) ]

Gene ID: 112081399, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112081399
Gene description
Sharpr-MPRA regulatory region 12058
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Feb 2018]
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Genomic context

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See LOC112081399 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 (48061357..48061651)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (48230903..48231197)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (48082909..48083203)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902844 Neighboring gene SEC61 translocon subunit beta pseudogene Neighboring gene Sharpr-MPRA regulatory region 14057 Neighboring gene Sharpr-MPRA regulatory region 4641 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:47968069-47969268 Neighboring gene Sharpr-MPRA regulatory region 13015 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:47995557-47996216 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47996217-47996876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3340 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:48015112-48015327 Neighboring gene GATA motif-containing MPRA enhancer 240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4711 Neighboring gene protein tyrosine phosphatase receptor type J Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4713 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:48050132-48050706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:48072419-48072920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:48072921-48073420 Neighboring gene Sharpr-MPRA regulatory region 8111 Neighboring gene NANOG hESC enhancer GRCh37_chr11:48077877-48078378 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:48092882-48093057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:48112153-48112964 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:48119178-48119678 Neighboring gene microRNA 3161 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:48149227-48149587 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:48198445-48198617 Neighboring gene NANOG hESC enhancer GRCh37_chr11:48212556-48213092 Neighboring gene olfactory receptor family 4 subfamily B member 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_056460.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    48061357..48061651
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    48230903..48231197
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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