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LOC122756374 Sharpr-MPRA regulatory region 15524 [ Homo sapiens (human) ]

Gene ID: 122756374, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122756374
Gene description
Sharpr-MPRA regulatory region 15524
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Sep 2021]
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Genomic context

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Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (9226480..9226774)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (9250263..9250557)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (9366609..9366903)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373416 Neighboring gene uncharacterized LOC105373415 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:9269636-9269796 Neighboring gene uncharacterized LOC105373417 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:9279832-9280332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:9282151-9283048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15275 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:9289685-9290604 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:9319676-9320875 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:9346090-9347022 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:9347023-9347953 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:9357948-9358822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:9371198-9371754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:9371755-9372309 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:9374524-9375723 Neighboring gene ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:9427423-9428622 Neighboring gene eukaryotic translation initiation factor 1 pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:9439781-9440280 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:9495983-9497182 Neighboring gene Sharpr-MPRA regulatory region 10317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:9513595-9514143 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:9514144-9514692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:9518857-9519441 Neighboring gene uncharacterized LOC124907730

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_076863.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    9226480..9226774
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    9250263..9250557
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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