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LOC123230394 Sharpr-MPRA regulatory region 12239 [ Homo sapiens (human) ]

Gene ID: 123230394, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123230394
Gene description
Sharpr-MPRA regulatory region 12239
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC123230394 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (152202980..152203274)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (154970884..154971178)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (151920769..151921063)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene AADACL2 antisense RNA 1 Neighboring gene uncharacterized LOC105374159 Neighboring gene MPRA-validated peak4862 silencer Neighboring gene uncharacterized LOC107986047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20703 Neighboring gene long intergenic non-protein coding RNA 2917 Neighboring gene uncharacterized LOC101928166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20705 Neighboring gene NANOG hESC enhancer GRCh37_chr3:151978898-151979587 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:151985921-151986763 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:151986764-151987605 Neighboring gene MBNL1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20707 Neighboring gene muscleblind like splicing regulator 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20708 Neighboring gene transmembrane protein 14E, 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_077338.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    152202980..152203274
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    154970884..154971178
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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