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LOC125177415 Sharpr-MPRA regulatory region 1803 [ Homo sapiens (human) ]

Gene ID: 125177415, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177415
Gene description
Sharpr-MPRA regulatory region 1803
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 17:Gen3', transcription 3' end of genes, highly expressed, more exonic). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
17p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (8488431..8488725)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (8394550..8394844)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory regions 4336 and 10869 Neighboring gene nudE neurodevelopment protein 1 like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8184 Neighboring gene MPRA-validated peak2716 silencer Neighboring gene MPRA-validated peak2717 silencer Neighboring gene Sharpr-MPRA regulatory region 9669 Neighboring gene uncharacterized LOC107987245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:8390687-8391187 Neighboring gene myosin heavy chain 10 Neighboring gene uncharacterized LOC102724262 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:8416542-8417741 Neighboring gene RNA, U7 small nuclear 43 pseudogene Neighboring gene Sharpr-MPRA regulatory region 10362 Neighboring gene Sharpr-MPRA regulatory region 2377 Neighboring gene peptidylprolyl isomerase A pseudogene 52

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_080472.1 

    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
    8488431..8488725
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    8394550..8394844
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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