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LOC124252638 Sharpr-MPRA regulatory region 8540 [ Homo sapiens (human) ]

Gene ID: 124252638, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124252638
Gene description
Sharpr-MPRA regulatory region 8540
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
9p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (37415012..37415306)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (37438709..37439003)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (37415009..37415303)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37385483-37385983 Neighboring gene long intergenic non-protein coding RNA 1627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28389 Neighboring gene Sharpr-MPRA regulatory region 4136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28391 Neighboring gene uncharacterized LOC124902154 Neighboring gene uncharacterized LOC105376035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28392 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37410141-37410932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37412515-37413305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37422039-37422664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37422665-37423290 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37424965-37425905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37428038-37428538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37428539-37429039 Neighboring gene glyoxylate and hydroxypyruvate reductase Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37434399-37435037 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 4 pseudogene 3 Neighboring gene zinc finger and BTB domain containing 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:37464369-37465054 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:37465055-37465740

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_078816.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    37415012..37415306
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    37438709..37439003
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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