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LOC128598890 CRISPRi-validated CCDC26, MYC and PVT1 e6 enhancer [ Homo sapiens (human) ]

Gene ID: 128598890, updated on 12-Sep-2024

Summary

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Gene symbol
LOC128598890
Gene description
CRISPRi-validated CCDC26, MYC and PVT1 e6 enhancer
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 represents an enhancer that was validated by reporter assays in K562 erythroleukemia cells. A subregion was also validated as a positively-acting cis-regulatory element for each of the CCDC26 (CCDC26 long non-coding RNA), MYC (MYC proto-oncogene, bHLH transcription factor) and PVT1 (Pvt1 oncogene) genes by CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Feb 2023]
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Genomic context

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See LOC128598890 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (129688360..129690572)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (130814343..130816551)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (130700606..130702818)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:130314706-130315206 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:130315207-130315707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27964 Neighboring gene RN7SK pseudogene 206 Neighboring gene MPRA-validated peak7173 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:130343219-130344418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27966 Neighboring gene CCDC26 long non-coding RNA Neighboring gene Sharpr-MPRA regulatory region 4396 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:130526802-130527734 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:130527735-130528668 Neighboring gene microRNA 3686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27969 Neighboring gene CRISPRi-validated CCDC26 and MYC e5 enhancer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:130598970-130600169 Neighboring gene MPRA-validated peak7175 silencer Neighboring gene VISTA enhancer hs1709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19540 Neighboring gene CRISPRi-validated CCDC26, MYC and PVT1 e7 enhancer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:130719165-130720364 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:130722337-130723536 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:130725004-130725177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27970 Neighboring gene mitochondrial translational release factor 1 like pseudogene 2 Neighboring gene gasdermin C Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:130844878-130845690 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:130845691-130846502 Neighboring gene ribosomal protein L15 pseudogene 12 Neighboring gene CYFIP related Rac1 interactor B

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. Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Fulco CP, et al. Science, 2016 Nov 11. PMID 27708057, Free PMC Article
  2. Genome-wide enhancer maps link risk variants to disease genes. Nasser J, et al. Nature, 2021 May. PMID 33828297, Free PMC Article
  3. 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_149613.1 

    Range
    101..2313
    Download
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    129688360..129690572
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    130814343..130816551
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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