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LOC122889069 Sharpr-MPRA regulatory region 12810 [ Homo sapiens (human) ]

Gene ID: 122889069, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122889069
Gene description
Sharpr-MPRA regulatory region 12810
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 DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122889069 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (38264798..38265092)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (38270511..38270805)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (38306289..38306583)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38179733-38180676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19681 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38196601-38197102 Neighboring gene uncharacterized LOC101928234 Neighboring gene MYD88 innate immune signal transduction adaptor Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:38205703-38206902 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38207186-38207801 Neighboring gene oxidative stress responsive kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14207 Neighboring gene Sharpr-MPRA regulatory region 5010 Neighboring gene solute carrier family 22 member 13 Neighboring gene CDC42 pseudogene 7 Neighboring gene solute carrier family 22 member 14 Neighboring gene RNA, U6 small nuclear 235, pseudogene

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_077203.1 

    Range
    101..395
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    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    38264798..38265092
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    38270511..38270805
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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