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LOC124900150 Sharpr-MPRA regulatory region 1645 [ Homo sapiens (human) ]

Gene ID: 124900150, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124900150
Gene description
Sharpr-MPRA regulatory region 1645
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 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
13q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (55517374..55517668)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (54733310..54733605)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903233 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:55519922-55520785 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:55574112-55574648 Neighboring gene long intergenic non-protein coding RNA 2335 Neighboring gene microRNA 5007 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:56010133-56010881 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:56011216-56011793 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:56150333-56150862 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:56151393-56151922 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:56152453-56152982 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:56157753-56158282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:56177964-56178464 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:56227375-56228088 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:56230739-56231635 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:56228945-56229842 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:56234325-56235221 Neighboring gene Sharpr-MPRA regulatory region 559 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:56538365-56538865 Neighboring gene hepatocyte nuclear factor 4 gamma pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:56685906-56686739 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:56686740-56687572 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:56688674-56689498 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:56689499-56690322 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:56740943-56741542 Neighboring gene spermatogenesis associated 2 pseudogene 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_079999.1 

    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    55517374..55517668
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    54733310..54733605
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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