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LOC125387306 Sharpr-MPRA regulatory region 8160 [ Homo sapiens (human) ]

Gene ID: 125387306, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125387306
Gene description
Sharpr-MPRA regulatory region 8160
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 DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, May 2022]
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Genomic context

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Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (53740570..53740864)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (55512738..55513032)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18122 Neighboring gene uncharacterized LOC105372672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18123 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:52238084-52238848 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:52243436-52243628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18130 Neighboring gene RNA, U7 small nuclear 14 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:52307857-52308356 Neighboring gene MPRA-validated peak4269 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18131 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:52327852-52328753 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:52328754-52329654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:52329655-52330556 Neighboring gene MPRA-validated peak4270 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:52340879-52341878 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:52341879-52342876 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:52345091-52345591 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18132 Neighboring gene MPRA-validated peak4271 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:52352121-52353026 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:52353027-52353930 Neighboring gene uncharacterized LOC124904933 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:52353931-52354834 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:52364790-52365383 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:52367327-52367828 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18135 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:52379320-52379986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18136 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:52384680-52385276 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:52390627-52391826 Neighboring gene MPRA-validated peak4272 silencer Neighboring gene MPRA-validated peak4274 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:52417835-52418336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18137 Neighboring gene HNF4 motif-containing MPRA enhancer 186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:52456215-52456785 Neighboring gene uncharacterized LOC124904934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13052 Neighboring gene uncharacterized LOC124904935

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_080981.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    53740570..53740864
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    55512738..55513032
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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