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LOC125177418 Sharpr-MPRA regulatory region 2542 [ Homo sapiens (human) ]

Gene ID: 125177418, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177418
Gene description
Sharpr-MPRA regulatory region 2542
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 24:Quies, heterochromatin/dead zone). [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 (9348552..9348846)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (9255537..9255831)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene netrin 1 Neighboring gene uncharacterized LOC101928266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9083413-9083914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9086141-9086640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9099203-9100124 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:9124521-9125720 Neighboring gene uncharacterized LOC124903923 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:9129517-9130068 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:9128413-9128964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9130069-9130619 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9131120-9131620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9133199-9133700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8197 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:9161269-9161860 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:9176317-9176818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11724 Neighboring gene NANOG hESC enhancer GRCh37_chr17:9225613-9226114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9232495-9233000 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:9233001-9233506 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:9233507-9234012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9234013-9234518 Neighboring gene syntaxin 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:9377307-9377808 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:9409688-9410556 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:9410557-9411424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11726 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11727 Neighboring gene ribosomal protein L19 pseudogene 18 Neighboring gene cilia and flagella associated protein 52 Neighboring gene uncharacterized LOC124903924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8198 Neighboring gene ubiquitin specific peptidase 43

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_080475.1 

    Range
    101..395
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    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
    9348552..9348846
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    9255537..9255831
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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