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LOC125387301 Sharpr-MPRA regulatory region 2265 [ Homo sapiens (human) ]

Gene ID: 125387301, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125387301
Gene description
Sharpr-MPRA regulatory region 2265
Gene type
biological region
Feature type(s)
regulatory: 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 repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125387301 in Genome Data Viewer
Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (51738970..51739264)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (53509800..53510094)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene nuclear factor of activated T cells 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50072771-50073376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50079139-50080099 Neighboring gene microRNA 3194 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:50103914-50105113 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50105077-50105578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18114 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:50149441-50150640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50157559-50158228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13041 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50186888-50187388 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:50224727-50225926 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:50226387-50226540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50240809-50241341 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:50247413-50248612 Neighboring gene Sharpr-MPRA regulatory region 9373 Neighboring gene ATPase phospholipid transporting 9A (putative) Neighboring gene Sharpr-MPRA regulatory region 11561 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:50315099-50315599 Neighboring gene Sharpr-MPRA regulatory region 2244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50318515-50319015 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:50321824-50322382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50323455-50323954 Neighboring gene NANOG hESC enhancer GRCh37_chr20:50327032-50327577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50329473-50329983 Neighboring gene Sharpr-MPRA regulatory region 2507 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50366388-50366998 Neighboring gene ribosomal protein L29 pseudogene 35 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50378781-50379465 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:50405511-50406010 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:50405009-50405510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50406470-50407036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50407037-50407602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50411851-50412350 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50415843-50416766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18116 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50417479-50418121 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:50418765-50419406 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:50427387-50428259 Neighboring gene spalt like transcription factor 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50463018-50463518 Neighboring gene long intergenic non-protein coding RNA 1429 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50478941-50479507

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

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_080976.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    51738970..51739264
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    53509800..53510094
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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