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LOC125146434 Sharpr-MPRA regulatory region 8309 [ Homo sapiens (human) ]

Gene ID: 125146434, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125146434
Gene description
Sharpr-MPRA regulatory region 8309
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125146434 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (25855068..25855362)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (26131493..26131787)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (25866389..25866683)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369297 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:25704024-25704524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:25704525-25705025 Neighboring gene heparan sulfate-glucosamine 3-sulfotransferase 4 Neighboring gene TNF receptor associated factor 7 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr16:25855925-25856182 Neighboring gene NANOG hESC enhancer GRCh37_chr16:25896223-25896797 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:25899968-25901167 Neighboring gene NANOG hESC enhancer GRCh37_chr16:25959776-25960299 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:25961820-25962673 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:25962674-25963526 Neighboring gene RNA, 5S ribosomal pseudogene 405 Neighboring gene microRNA 548w

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_080360.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    25855068..25855362
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    26131493..26131787
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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