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LOC122889068 Sharpr-MPRA regulatory region 2528 [ Homo sapiens (human) ]

Gene ID: 122889068, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122889068
Gene description
Sharpr-MPRA regulatory region 2528
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Oct 2021]
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Genomic context

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Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (37905998..37906292)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (37910161..37910455)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (37947489..37947783)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene integrin subunit alpha 9 Neighboring gene VISTA enhancer hs1961 Neighboring gene ribosomal protein L21 pseudogene 135 Neighboring gene ITGA9 antisense RNA 1 Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 4 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37904633-37905134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37905135-37905634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:37945100-37945826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19674 Neighboring gene CTD small phosphatase like Neighboring gene HNF1 motif-containing MPRA enhancer 248 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:38003356-38003967 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38010565-38011128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38011129-38011690 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:38028477-38028654 Neighboring gene Sharpr-MPRA regulatory region 12639 Neighboring gene Sharpr-MPRA regulatory region 7921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38035775-38036392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38039104-38039674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14201 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38047479-38047979 Neighboring gene microRNA 26a-1 Neighboring gene villin like

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_077200.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    37905998..37906292
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    37910161..37910455
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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