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LOC125146431 Sharpr-MPRA regulatory region 8464 [ Homo sapiens (human) ]

Gene ID: 125146431, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125146431
Gene description
Sharpr-MPRA regulatory region 8464
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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Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (24138088..24138382)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (24414612..24414906)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23716303-23716803 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:23740522-23741453 Neighboring gene polo like kinase 1 Neighboring gene endoplasmic reticulum to nucleus signaling 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:23766235-23766880 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:23797941-23798576 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:23798577-23799212 Neighboring gene CRISPRi-validated cis-regulatory element chr16.1865 Neighboring gene calcineurin like EF-hand protein 2 Neighboring gene CRISPRi-validated cis-regulatory element chr16.1866 Neighboring gene CRISPRi-validated cis-regulatory element chr16.1867 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23846913-23847460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23847461-23848006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10589 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10590 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:23858657-23858875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10591 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:23877081-23877727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10592 Neighboring gene protein kinase C beta Neighboring gene GATA motif-containing MPRA enhancer 73 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:23915426-23915611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10593 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10595 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10596 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10597 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10598 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:24066265-24066934 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr16:24086836-24087648 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr16:24087649-24088461 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:24119013-24119512 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:24146937-24147472 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:24148009-24148544 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:24148545-24149080 Neighboring gene NANOG hESC enhancer GRCh37_chr16:24219906-24220465 Neighboring gene microRNA 1273h Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:24257631-24258830 Neighboring gene long intergenic non-protein coding RNA 2194

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_080357.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    24138088..24138382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    24414612..24414906
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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