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LOC128462386 CRISPRi-FlowFISH-validated PFKFB3 regulatory element GRCh37_chr10:6389972-6390472 [ Homo sapiens (human) ]

Gene ID: 128462386, updated on 12-Sep-2024

Summary

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Gene symbol
LOC128462386
Gene description
CRISPRi-FlowFISH-validated PFKFB3 regulatory element GRCh37_chr10:6389972-6390472
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 positively-acting cis-regulatory element for the PFKFB3 (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in Jurkat T cells. [provided by RefSeq, Feb 2023]
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Genomic context

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See LOC128462386 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (6348010..6348510)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (6348218..6348718)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (6389972..6390472)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2967 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:6340850-6342049 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:6356348-6356848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:6356849-6357349 Neighboring gene syndecan binding protein pseudogene 1 Neighboring gene long intergenic non-protein coding RNA 2649 Neighboring gene developmental pluripotency associated 5 pseudogene 3 Neighboring gene long intergenic non-protein coding RNA 2656 Neighboring gene uncharacterized LOC124902370 Neighboring gene NANOG hESC enhancer GRCh37_chr10:6452056-6452557 Neighboring gene protein kinase C theta

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

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 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_149574.1 

    Range
    101..601
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    6348010..6348510
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    6348218..6348718
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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