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LOC125177508 Sharpr-MPRA regulatory region 10137 [ Homo sapiens (human) ]

Gene ID: 125177508, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177508
Gene description
Sharpr-MPRA regulatory region 10137
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (51093848..51094142)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (51961180..51961474)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:49021226-49022109 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:49022110-49022992 Neighboring gene uncharacterized LOC124904029 Neighboring gene Sharpr-MPRA regulatory region 1122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:49029041-49029542 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:49031243-49032442 Neighboring gene sperm associated antigen 9 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:49175960-49176460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8721 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12398 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:49198151-49198965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12400 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:49205455-49205678 Neighboring gene MPRA-validated peak2888 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr17:49219886-49220387 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:49222416-49222916 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:49230233-49231432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:49232587-49233118 Neighboring gene NME1-NME2 readthrough Neighboring gene NME/NM23 nucleoside diphosphate kinase 1

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_080563.1 

    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
    51093848..51094142
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    51961180..51961474
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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