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LOC125316778 Sharpr-MPRA regulatory region 8649 [ Homo sapiens (human) ]

Gene ID: 125316778, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125316778
Gene description
Sharpr-MPRA regulatory region 8649
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 15:Elon, transcription elongation, stronger H3K36me3, more exonic) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 17:Gen3', transcription 3' end of genes, highly expressed, more exonic). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125316778 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (67353953..67354247)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (68229859..68230153)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA8 Neighboring gene RNA, 5S ribosomal pseudogene 447 Neighboring gene MPRA-validated peak2951 silencer Neighboring gene MPRA-validated peak2952 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:65323222-65323938 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:65326873-65327713 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12622 Neighboring gene proteasome 26S subunit, non-ATPase 12 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8869 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:65373203-65373896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8872 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8874 Neighboring gene uncharacterized LOC124904047 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12623 Neighboring gene Sharpr-MPRA regulatory region 1189 Neighboring gene phosphatidylinositol transfer protein cytoplasmic 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:65403298-65404268 Neighboring gene small nucleolar RNA U13

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_080597.1 

    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
    67353953..67354247
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    68229859..68230153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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