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LOC128462408 CRISPRi-FlowFISH-validated PFKFB3 regulatory elements GRCh37_chr10:6186610-6187110 and GRCh37_chr10:6186666-6187166 [ Homo sapiens (human) ]

Gene ID: 128462408, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128462408
Gene description
CRISPRi-FlowFISH-validated PFKFB3 regulatory elements GRCh37_chr10:6186610-6187110 and GRCh37_chr10:6186666-6187166
Gene type
biological region
Feature type(s)
regulatory: silencer, 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, which includes the 5' end of the PFKFB3 (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3) gene, 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. Two overlapping subregions were validated as positively-acting cis-regulatory elements for PFKFB3 based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in either Jurkat T cells, or THP-1 monocytic cells. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (6144633..6145203)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (6144819..6145389)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2097 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2098 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:6131655-6132493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:6137781-6138282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:6138283-6138782 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:6138886-6139486 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:6149773-6150468 Neighboring gene RNA binding motif protein 17 Neighboring gene MPRA-validated peak861 silencer Neighboring gene uncharacterized LOC101928080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:6176097-6176645 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:6176646-6177193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2957 Neighboring gene uncharacterized LOC124902369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2958 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2961 Neighboring gene RN7SK pseudogene 78 Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 Neighboring gene microRNA 3155a Neighboring gene microRNA 3155b

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-wide enhancer maps link risk variants to disease genes. Nasser J, et al. Nature, 2021 May. PMID 33828297, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 2100
  • CRISPRi-FlowFISH-validated PFKFB3 regulatory element GRCh37_chr10:6186610-6187110
  • CRISPRi-FlowFISH-validated PFKFB3 regulatory element GRCh37_chr10:6186666-6187166

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_149596.2 

    Range
    101..671
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    6144633..6145203
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    6144819..6145389
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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