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LOC124416849 Sharpr-MPRA regulatory region 8551 [ Homo sapiens (human) ]

Gene ID: 124416849, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124416849
Gene description
Sharpr-MPRA regulatory region 8551
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 19:H4K20, transcription, primarily H4K20me1, more intronic). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (77877431..77877725)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (78746499..78746793)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (79637189..79637483)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1266, pseudogene Neighboring gene inosine monophosphate dehydrogenase 1 pseudogene 5 Neighboring gene discs large MAGUK scaffold protein 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:79568517-79569016 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:79591709-79592210 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:79592211-79592710 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:79596052-79596324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:79596746-79597366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:79601269-79601770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:79613571-79614072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:79614073-79614572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:79616089-79616612 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:79616613-79617136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:79623439-79624198 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:79625716-79626473 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:79627013-79628212 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:79637563-79638502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:79649557-79650232 Neighboring gene uncharacterized LOC101929347 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:79651583-79652256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:79660915-79661442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:79661443-79661970 Neighboring gene Sharpr-MPRA regulatory region 4447 Neighboring gene NFE2L2 motif-containing MPRA enhancers 69 and 123 Neighboring gene RNA, 7SL, cytoplasmic 284, pseudogene

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

See Variation Viewer (GRCh37.p13)

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_079070.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    77877431..77877725
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    78746499..78746793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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