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LOC125048447 Sharpr-MPRA regulatory region 8364 [ Homo sapiens (human) ]

Gene ID: 125048447, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125048447
Gene description
Sharpr-MPRA regulatory region 8364
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 DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (76917186..76917480)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (71126921..71127215)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ribosomal protein L22 pseudogene 2 Neighboring gene RN7SK pseudogene 17 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:77370757-77371956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8774 Neighboring gene VISTA enhancer hs1466 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77389998-77390993 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77390994-77391988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:77393097-77394053 Neighboring gene uncharacterized LOC124903349 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr14:77401173-77401771 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr14:77401772-77402369 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:77406282-77406782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8776 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77419449-77420018 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77420019-77420588 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8777 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:77422669-77423203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8778 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8779 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77426954-77427488 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77427489-77428024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8781 Neighboring gene Sharpr-MPRA regulatory region 14350 Neighboring gene long intergenic non-protein coding RNA 1629

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_080143.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    76917186..76917480
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    71126921..71127215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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