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LOC122756383 Sharpr-MPRA regulatory region 12680 [ Homo sapiens (human) ]

Gene ID: 122756383, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122756383
Gene description
Sharpr-MPRA regulatory region 12680
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 6:EnhF, candidate strong enhancer, flanking open chromatin). [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 (11901563..11901857)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (11930418..11930710)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (12041689..12041983)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene lipin 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:11919054-11920253 Neighboring gene Sharpr-MPRA regulatory region 7856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15325 Neighboring gene microRNA 548s Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:11970167-11970883 Neighboring gene uncharacterized LOC105373430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15327 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15329 Neighboring gene microRNA 4262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15331 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15333 Neighboring gene Sharpr-MPRA regulatory region 524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15334 Neighboring gene small nucleolar RNA SNORD18 Neighboring gene MIR3681 host gene Neighboring gene ST13, Hsp70 interacting protein pseudogene 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

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_076872.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    11901563..11901857
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    11930418..11930710
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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