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Alpha-re alpha-globin locus regulatory region [ Mus musculus (house mouse) ]

Gene ID: 106821731, updated on 9-Aug-2024

Summary

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Gene symbol
Alpha-re
Gene description
alpha-globin locus regulatory region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: DNase_I_hypersensitive_site, enhancer
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
alpha-MRE
Summary
This genomic region represents the regulatory region that exists upstream of the mouse alpha-globin gene cluster. It is orthologous to the human alpha-globin locus control region (LCR), which regulates developmental stage- and erythroid lineage-specific expression of the embryonic and adult alpha-globin genes. This region overlaps the Nprl3 (nitrogen permease regulator-like 3) gene, which is transcribed in the opposite orientation compared to the downstream alpha-globin genes, and it also overlaps the 3' end of the Mpg (N-methylpurine-DNA glycosylase) gene. Like the human ortholog, this mouse region is characterized by several DNase I hypersensitive sites (HSs), including the conserved erythroid-specific sites HS-8, HS-21, HS-26 and HS-31. Mouse HS-26 is orthologous to human HS-40, which is the major regulatory element in human. However, unlike human HS-40, mouse HS-26 has relatively weak enhancer activity and does not have LCR activity, suggesting that additional cis-acting elements are necessary for complete developmental regulation of the alpha-globin genes in mice. Five enhancer-like elements, R1, R2, R3, Rm and R4, which correlate with the HSs and/or ATAC-seq accessible sites, are located in this region. Together they constitute a super-enhancer, where each constituent enhancer acts in an additive manner to regulate developmental expression of the alpha-globin genes. Similar to the human counterpart, this mouse upstream regulatory region forms an active chromatin hub based on observed looping interactions with the active alpha-globin genes. [provided by RefSeq, May 2017]
Orthologs
human all
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Genomic context

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See Alpha-re in Genome Data Viewer
Location:
11 A4
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (32181303..32220102)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (32231303..32270102)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E730 Neighboring gene small nuclear ribonucleoprotein 25 (U11/U12) Neighboring gene rhomboid 5 homolog 1 Neighboring gene STARR-positive B cell enhancer ABC_E11473 Neighboring gene N-methylpurine-DNA glycosylase Neighboring gene nitrogen permease regulator-like 3 Neighboring gene hemoglobin X, alpha-like embryonic chain in Hba complex Neighboring gene hemoglobin alpha, adult chain 1

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. Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. Vierstra J, et al. Science, 2014 Nov 21. PMID 25411453, Free PMC Article
  2. Uncovering enhancer functions using the α-globin locus. Vernimmen D. PLoS Genet, 2014 Oct. PMID 25330308, Free PMC Article
  3. Genetic dissection of the α-globin super-enhancer in vivo. Hay D, et al. Nat Genet, 2016 Aug. PMID 27376235, Free PMC Article
  4. Evolution of hemoglobin and its genes. Hardison RC. Cold Spring Harb Perspect Med, 2012 Dec 1. PMID 23209182, Free PMC Article
  5. Active chromatin hub of the mouse alpha-globin locus forms in a transcription factory of clustered housekeeping genes. Zhou GL, et al. Mol Cell Biol, 2006 Jul. PMID 16782894, Free PMC Article

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Other Names

  • VISTA enhancer mm101
  • alpha-globin locus control region
  • alpha-globin super-enhancer
  • alpha-locus controlling region
  • alpha-major regulatory element

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_046313.1 

    Range
    101..38900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    32181303..32220102
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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