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LOC112272582 Sharpr-MPRA regulatory region 5138 [ Homo sapiens (human) ]

Gene ID: 112272582, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112272582
Gene description
Sharpr-MPRA regulatory region 5138
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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). It also displayed weak repressive activity in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Mar 2018]
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Genomic context

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See LOC112272582 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (31236506..31236800)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (29030581..29030875)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (31528709..31529003)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903454 Neighboring gene long intergenic non-protein coding RNA 2352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31517937-31518509 Neighboring gene long intergenic non-protein coding RNA 3034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31548124-31548696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31570698-31571198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31571199-31571699 Neighboring gene KLF13-II enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31594474-31595156 Neighboring gene KLF13-III enhancer Neighboring gene VISTA enhancer hs2231 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31604403-31605163 Neighboring gene KLF13 promoter region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31621870-31622434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31627858-31628358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31628359-31628859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31634092-31634903 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31634904-31635714 Neighboring gene KLF transcription factor 13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31649687-31650186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31666033-31667020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6267 Neighboring gene uncharacterized LOC105370939 Neighboring gene ubiquitin conjugating enzyme E2 C pseudogene 4

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_056719.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    31236506..31236800
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332701.1 Reference GRCh38.p14 PATCHES

    Range
    3409837..3410131
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_187660.1 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    3522289..3522583
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    29030581..29030875
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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