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LOC124625874 Sharpr-MPRA regulatory region 13378 [ Homo sapiens (human) ]

Gene ID: 124625874, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124625874
Gene description
Sharpr-MPRA regulatory region 13378
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 non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 12:CtcfO). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
11q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (133134594..133134888)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (133175067..133175361)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene opioid binding protein/cell adhesion molecule like Neighboring gene uncharacterized LOC124902819 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:132483305-132484504 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:132502505-132503704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:132513245-132513744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:132551286-132551786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:132551787-132552287 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:132755960-132756466 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:132780259-132781458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:132789928-132790505 Neighboring gene uncharacterized LOC105369580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:132930114-132930614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:132934609-132935182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4085 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133085747-133086246 Neighboring gene uncharacterized LOC124902796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5766 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:133207744-133208254 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:133230716-133231216 Neighboring gene OPCML intronic transcript 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_079474.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    133134594..133134888
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    133175067..133175361
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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