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LOC123620059 Sharpr-MPRA regulatory region 14615 [ Homo sapiens (human) ]

Gene ID: 123620059, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123620059
Gene description
Sharpr-MPRA regulatory region 14615
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, Dec 2021]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (15550998..15551292)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (15424178..15424472)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (15551229..15551523)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene jumonji and AT-rich interaction domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16951 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24075 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15337209-15337728 Neighboring gene RNA, U6 small nuclear 645, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15385480-15386240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24079 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15402869-15403369 Neighboring gene Sharpr-MPRA regulatory region 1760 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15404593-15405283 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15413673-15413840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24081 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15444755-15445255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15447999-15448499 Neighboring gene NANOG hESC enhancer GRCh37_chr6:15461204-15461861 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15469722-15469904 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:15473668-15474867 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:15491921-15492422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15507577-15508118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15508119-15508660 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:15508661-15509202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15513022-15514000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15517558-15518058 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15523265-15523451 Neighboring gene uncharacterized LOC105374947 Neighboring gene MPRA-validated peak5680 silencer Neighboring gene uncharacterized LOC124901267 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15551965-15552513 Neighboring gene dystrobrevin binding protein 1 Neighboring gene MPRA-validated peak5681 silencer Neighboring gene MPRA-validated peak5682 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24083 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24085 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24086 Neighboring gene MPRA-validated peak5684 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15641694-15641884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24087 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16953 Neighboring gene MPRA-validated peak5686 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15725723-15726536 Neighboring gene uncharacterized LOC102724520 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:15745025-15745698 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:15745699-15746372 Neighboring gene MPRA-validated peak5688 silencer Neighboring gene MPRA-validated peak5689 silencer Neighboring gene uncharacterized LOC105374948

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_077941.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    15550998..15551292
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    15424178..15424472
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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