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LOC116309148 CRISPRi-validated cis-regulatory element chrX.477 [ Homo sapiens (human) ]

Gene ID: 116309148, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116309148
Gene description
CRISPRi-validated cis-regulatory element chrX.477
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 represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. It was validated as a cis-regulatory element for the SAT1 (spermidine/spermine N1-acetyltransferase 1) gene on chromosome X based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2019]
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Genomic context

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Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (24231108..24231459)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (23815296..23815641)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (24249225..24249576)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA68 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29499 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:24167489-24168302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29500 Neighboring gene ZFX antisense RNA 1 Neighboring gene zinc finger protein X-linked Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:24328768-24329520 Neighboring gene SUPT20H like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:24382719-24383459 Neighboring gene SUPT20H like 1

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_067115.1 

    Range
    101..452
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    24231108..24231459
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    23815296..23815641
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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