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LOC124819388 Sharpr-MPRA regulatory region 11062 [ Homo sapiens (human) ]

Gene ID: 124819388, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124819388
Gene description
Sharpr-MPRA regulatory region 11062
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 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124819388 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (106131631..106131925)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (106094394..106094688)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ST13, Hsp70 interacting protein pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106474669-106475169 Neighboring gene NUAK family kinase 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:106492406-106492991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106494441-106494974 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106500655-106501400 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106501401-106502144 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106502145-106502889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106508970-106509546 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106509547-106510123 Neighboring gene uncharacterized LOC124903007 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106523693-106524442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106524443-106525192 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:106526214-106527056 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106527057-106527900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106527901-106528743 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:106531161-106531662 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:106534054-106534673 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106541977-106542476 Neighboring gene thyroid hormone receptor interactor 11 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106581756-106582590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106605939-106606439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4814 Neighboring gene cytoskeleton associated protein 4

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_079805.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    106131631..106131925
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    106094394..106094688
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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