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LOC125146419 Sharpr-MPRA regulatory region 7034 [ Homo sapiens (human) ]

Gene ID: 125146419, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125146419
Gene description
Sharpr-MPRA regulatory region 7034
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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125146419 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 (15653312..15653606)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (15658218..15658512)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (15747169..15747463)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene meiosis regulator and mRNA stability factor 1 Neighboring gene uncharacterized LOC124903649 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15743803-15744304 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15744305-15744804 Neighboring gene microRNA 484 Neighboring gene nudE neurodevelopment protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15766651-15767392 Neighboring gene Sharpr-MPRA regulatory region 12074 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15814393-15815196 Neighboring gene myosin heavy chain 11 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15830279-15831035 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15851025-15851658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15851659-15852292 Neighboring gene uncharacterized LOC124903650 Neighboring gene uncharacterized LOC124903651

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_080344.1 

    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
    15653312..15653606
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187607.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    1311323..1311617
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    15658218..15658512
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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