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LOC124416926 Sharpr-MPRA regulatory region 15643 [ Homo sapiens (human) ]

Gene ID: 124416926, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124416926
Gene description
Sharpr-MPRA regulatory region 15643
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, 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 (123884193..123884487)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (124761100..124761394)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (125643709..125644003)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:125488883-125489382 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:125506649-125507630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:125520224-125521126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:125521127-125522029 Neighboring gene carboxypeptidase X, M14 family member 2 Neighboring gene uncharacterized LOC105378533 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:125541445-125542192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:125619193-125619693 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:125623194-125623935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:125625482-125626289 Neighboring gene uncharacterized LOC105378534 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:125685728-125686927 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_10738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:125707945-125708625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:125710066-125710566 Neighboring gene uncharacterized LOC107984128 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_10754 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_10761 and experimental_10770

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_079142.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    123884193..123884487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    124761100..124761394
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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