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LOC128669075 CRISPRi-validated MYB cis-regulatory element XLOC_042889 [ Homo sapiens (human) ]

Gene ID: 128669075, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128669075
Gene description
CRISPRi-validated MYB cis-regulatory element XLOC_042889
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 sequence overlaps the 5' end of the LOC124901407 long non-coding RNA (lncRNA) gene on chromosome 6. It was validated as a positively-acting cis-regulatory element for the MYB (MYB proto-oncogene, transcription factor) gene based on CRISPR/Cas9-mediated perturbation in K562 erythroleukemia cells. [provided by RefSeq, Feb 2023]
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Genomic context

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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (135323327..135323474)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (136511614..136511761)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25104 Neighboring gene MYB proto-oncogene, transcription factor Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:135570900-135572099 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:135573042-135573542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:135573543-135574043 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:135577907-135579106 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:135585007-135585209 Neighboring gene microRNA 548a-2 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:135591948-135592842 Neighboring gene VISTA enhancer hs1351 Neighboring gene uncharacterized LOC124901407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25105 Neighboring gene Sharpr-MPRA regulatory region 12318 Neighboring gene Abelson helper integration site 1 Neighboring gene beta-transducin repeat containing E3 ubiquitin protein ligase pseudogene 1 Neighboring gene MPRA-validated peak6137 silencer Neighboring gene MPRA-validated peak6138 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25106 Neighboring gene MPRA-validated peak6140 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17570 Neighboring gene AHI1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17571 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:135921214-135922413 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene 73

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. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Liu SJ, et al. Science, 2017 Jan 6. PMID 27980086, 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

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_149641.1 

    Range
    101..248
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    135323327..135323474
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    136511614..136511761
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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