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LOC125177309 Sharpr-MPRA regulatory region 1297 [ Homo sapiens (human) ]

Gene ID: 125177309, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177309
Gene description
Sharpr-MPRA regulatory region 1297
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 21:Repr, strong Polycomb repression). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177309 in Genome Data Viewer
Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (50733518..50733812)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (56531152..56531446)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927272 Neighboring gene sorting nexin 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10821 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7489 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10825 Neighboring gene Sharpr-MPRA regulatory region 14141 Neighboring gene nucleotide binding oligomerization domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7490 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:50743936-50744141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10826 Neighboring gene CYLD antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10827 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7491 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10828 Neighboring gene microRNA 3181 Neighboring gene CYLD lysine 63 deubiquitinase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7492 Neighboring gene CYLD antisense RNA 2

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_080377.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    50733518..50733812
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    56531152..56531446
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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