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LOC125177342 Sharpr-MPRA regulatory region 9240 [ Homo sapiens (human) ]

Gene ID: 125177342, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177342
Gene description
Sharpr-MPRA regulatory region 9240
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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (68390506..68390800)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (74186333..74186627)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene protein arginine methyltransferase 7 Neighboring gene RNA, U4 small nuclear 30, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:68382607-68383107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11013 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68396471-68397283 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68397284-68398095 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68400892-68401445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68401446-68401998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11015 Neighboring gene sphingomyelin phosphodiesterase 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68413436-68413938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68413939-68414439 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68415806-68416642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68416643-68417477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68422765-68423592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68431713-68432213 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68432795-68433424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68433425-68434052 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68442570-68443549 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68444678-68445630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68445631-68446581 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11016 Neighboring gene uncharacterized LOC124903705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68504627-68505126 Neighboring gene ribosomal protein L35a pseudogene 33

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_080410.1 

    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
    68390506..68390800
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    74186333..74186627
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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