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LOC108449898 enhancer-blocking elements downstream of IL3 [ Homo sapiens (human) ]

Gene ID: 108449898, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108449898
Gene description
enhancer-blocking elements downstream of IL3
Gene type
biological region
Feature type(s)
regulatory: enhancer, enhancer_blocking_element, insulator
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 is located just downstream of the IL3 (interleukin 3) gene on chromosome 5. Three overlapping fragments within this region, 5-1-1, 5-1-2 and 5-1-3, were identified as putative enhancer-blocking chromatin insulators based on CTCF association and DNase I hypersensitivity in multiple cell types by ChIP-seq and genome-wide chromatin accessibility assays. Each subregion was validated as an enhancer-blocking element based on its ability to block activity of an enhancer when positioned between the enhancer and a promoter in a lentiviral reporter assay. In addition, the central 5-1-2 fragment functioned as a barrier insulator based on its ability to reduce retroviral vector genotoxicity in a mouse in vivo tumor formation model. Another subregion was also validated as an enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC108449898 in Genome Data Viewer
Location:
5q31.1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (132063480..132065722)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (132583349..132585591)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (131399173..131401171)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene acyl-CoA synthetase long chain family member 6 Neighboring gene uncharacterized LOC124901062 Neighboring gene MPRA-validated peak5463 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16311 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131366011-131366190 Neighboring gene uncharacterized LOC105379174 Neighboring gene origin of replication downstream of CSF2 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131423316-131423538 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:131429841-131431040 Neighboring gene interleukin 3 Neighboring gene Sharpr-MPRA regulatory region 12197 Neighboring gene Sharpr-MPRA regulatory region 14284 Neighboring gene colony stimulating factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131517361-131517888 Neighboring gene NANOG hESC enhancer GRCh37_chr5:131520231-131520732 Neighboring gene Sharpr-MPRA regulatory region 7421 Neighboring gene P4HA2 antisense RNA 1 Neighboring gene prolyl 4-hydroxylase subunit alpha 2

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. Identification and characterization of enhancer-blocking insulators to reduce retroviral vector genotoxicity. Groth AC, et al. PLoS One, 2013. PMID 24098520, Free PMC Article
  2. Widespread plasticity in CTCF occupancy linked to DNA methylation. Wang H, et al. Genome Res, 2012 Sep. PMID 22955980, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  4. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • H3K4me1 hESC enhancer GRCh37_chr5:131400909-131401415
  • chromatin insulators 5-1-1, 5-1-2 and 5-1-3

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_051339.2 

    Range
    101..2343
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    132063480..132065722
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    132583349..132585591
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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