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LOC125177489 Sharpr-MPRA regulatory region 15390 [ Homo sapiens (human) ]

Gene ID: 125177489, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177489
Gene description
Sharpr-MPRA regulatory region 15390
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44350781..44351075)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (45204780..45205074)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 39 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8588 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8589 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12255 Neighboring gene uncharacterized LOC124904009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42403114-42403965 Neighboring gene CRISPRi-validated cis-regulatory element chr17.2878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42420716-42421641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12260 Neighboring gene granulin precursor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8590 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8591 Neighboring gene family with sequence similarity 171 member A2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42438205-42438805 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42438806-42439405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8592 Neighboring gene RPL7L1 pseudogene 5

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_080544.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    44350781..44351075
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    45204780..45205074
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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