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LOC125177381 Sharpr-MPRA regulatory region 15454 [ Homo sapiens (human) ]

Gene ID: 125177381, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125177381
Gene description
Sharpr-MPRA regulatory region 15454
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 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177381 in Genome Data Viewer
Location:
16q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (85160503..85160797)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (91226608..91226902)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (85194109..85194403)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85159272-85159794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85159795-85160316 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85170709-85171641 Neighboring gene uncharacterized LOC105371382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85180218-85180762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85180763-85181307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85187102-85187602 Neighboring gene long intergenic non-protein coding RNA 2139 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85204591-85205300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85205301-85206012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85221161-85222101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85224026-85224526 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:85233339-85234538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85234576-85235312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85240619-85241362 Neighboring gene Sharpr-MPRA regulatory region 3131 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85248283-85248783 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85254771-85255472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85255473-85256172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11265 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:85259454-85259616 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85261597-85262172 Neighboring gene Gse1 coiled-coil protein Neighboring gene ReSE screen-validated silencer GRCh37_chr16:85267436-85267602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85267685-85268542 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7802 Neighboring gene microRNA 12128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85272407-85272982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85274317-85275021 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85292052-85292756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85292757-85293460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85293461-85294165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85300159-85300706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85303550-85304252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85305185-85306181 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85308847-85309819 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85309820-85310793 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85310794-85311766 Neighboring gene cytochrome c oxidase subunit 6C pseudogene 16

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_080438.1 

    Range
    101..395
    Download
    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
    85160503..85160797
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    91226608..91226902
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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