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LOC125110345 Sharpr-MPRA regulatory region 14643 [ Homo sapiens (human) ]

Gene ID: 125110345, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125110345
Gene description
Sharpr-MPRA regulatory region 14643
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression) and 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:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (66647771..66648065)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (64469361..64469655)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:66795563-66796062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9616 Neighboring gene small nucleolar RNA, C/D box 18A Neighboring gene zwilch kinetochore protein Neighboring gene ribosomal protein L4 Neighboring gene Sharpr-MPRA regulatory region 674 Neighboring gene lactase like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:66886299-66886800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:66886801-66887300 Neighboring gene long intergenic non-protein coding RNA 1169 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:66909444-66910022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:66910023-66910601 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:66914309-66914837 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:66914838-66915365 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:66965231-66965789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:66965790-66966347 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:66969772-66970272 Neighboring gene Sharpr-MPRA regulatory region 4382 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:66992708-66993208 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:66993253-66993439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6568 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6567 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:66998965-66999484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:67004109-67004608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:67014656-67015156 Neighboring gene SMAD family member 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:67026431-67026931 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:67034899-67035399 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67036859-67037484 Neighboring gene Sharpr-MPRA regulatory region 14210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:67050021-67050579 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:67055291-67056020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67057907-67058476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67058477-67059045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:67062107-67062668 Neighboring gene HNF4 motif-containing MPRA enhancer 143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9617 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67094295-67094840 Neighboring gene leucine zipper and EF-hand containing transmembrane protein 1 pseudogene 1

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_080245.1 

    Range
    101..395
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    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    66647771..66648065
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    64469361..64469655
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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