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LOC122152305 Sharpr-MPRA regulatory region 14236 [ Homo sapiens (human) ]

Gene ID: 122152305, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122152305
Gene description
Sharpr-MPRA regulatory region 14236
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 17:Gen3', transcription 3' end of genes, highly expressed, more exonic). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (223748107..223748401)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (222937835..222938129)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (223935809..223936103)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373281 Neighboring gene RNA, U6 small nuclear 1248, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:223888788-223889634 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:223894361-223895560 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:223895561-223896060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2591 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:223899927-223900878 Neighboring gene calpain 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5382 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:223906461-223907308 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:223915193-223915853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:223919231-223919826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:223921601-223922461 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:223926031-223926546 Neighboring gene uncharacterized LOC105373046 Neighboring gene Sharpr-MPRA regulatory region 3187 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:223939947-223941146 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:223959947-223960602 Neighboring gene uncharacterized LOC105373041 Neighboring gene tumor protein p53 binding protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1844

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_076579.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    223748107..223748401
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    222937835..222938129
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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