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LOC119407421 CRISPRi-FlowFISH-validated PLP2 regulatory element 13 [ Homo sapiens (human) ]

Gene ID: 119407421, updated on 12-Sep-2024

Summary

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Gene symbol
LOC119407421
Gene description
CRISPRi-FlowFISH-validated PLP2 regulatory element 13
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 PLP2 (proteolipid protein 2) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. [provided by RefSeq, Nov 2020]
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Genomic context

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See LOC119407421 in Genome Data Viewer
Location:
Xp
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (49193388..49193908)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (48605246..48605766)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (49049845..49050365)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20837 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:49022309-49023254 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 10 Neighboring gene MAGI family member, X-linked Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20838 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20839 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:49032849-49033350 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 11 Neighboring gene prickle planar cell polarity protein 3 Neighboring gene proteolipid protein 2 Neighboring gene CRISPRi-FlowFISH-validated GATA1 and PLP2 regulatory element Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 12 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29635 Neighboring gene synaptophysin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20843 Neighboring gene SYP antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:49065732-49066931 Neighboring gene calcium voltage-gated channel subunit alpha1 F Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:49086994-49087652

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_070991.1 

    Range
    101..621
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    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    49193388..49193908
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    48605246..48605766
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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