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LOC117038772 CRISPRi-FlowFISH-validated RPN1 regulatory element 3 [ Homo sapiens (human) ]

Gene ID: 117038772, updated on 10-Oct-2023

Summary

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Gene symbol
LOC117038772
Gene description
CRISPRi-FlowFISH-validated RPN1 regulatory element 3
Gene type
biological region
Feature type(s)
regulatory: transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region was predicted to be an enhancer based on an activity-by-contact (ABC) model that predicts enhancer-gene connections, where the putative enhancer strength is measured by DNase I hypersensitivity and H3K27 acetylation, and the contact frequency by Hi-C. It was validated as a negatively-acting cis-regulatory element for the RPN1 (ribophorin I) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. [provided by RefSeq, Mar 2020]
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Genomic context

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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (128532862..128533362)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (131274428..131274928)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (128251705..128252205)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene CRISPRi-FlowFISH-validated H1-10 regulatory element 2 Neighboring gene GATA binding protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128208361-128209172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128209173-128209982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14707 Neighboring gene GATA2 antisense RNA 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:128223035-128224234 Neighboring gene uncharacterized LOC90246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128243441-128243940 Neighboring gene transmembrane p24 trafficking protein 10 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128266479-128266979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128285743-128286421 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128287100-128287778 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128287779-128288455 Neighboring gene long intergenic non-protein coding RNA 1565

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. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Fulco CP, et al. Nat Genet, 2019 Dec. PMID 31784727, 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_068098.1 

    Range
    101..601
    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
    128532862..128533362
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    131274428..131274928
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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