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LOC108663984 ALAS2 intron 1 and 3 erythroid regulatory elements [ Homo sapiens (human) ]

Gene ID: 108663984, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108663984
Gene description
ALAS2 intron 1 and 3 erythroid regulatory elements
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer, 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 regions represents regulatory elements located in 5' introns of the ALAS2 (5'-aminolevulinate synthase 2) gene on chromosome X. One element, which spans intron 1, was validated as a functional enhancer by reporter assays in both human K562 erythroleukemia and murine erythroleukemia (MEL) cells. A subregion, which includes a GATA1 binding motif, was validated as a positively-acting cis-regulatory element for ALAS2 based on CRISPR/Cas9-mediated perturbation in K562 cells. Another element spanning intron 3 functioned as a silencer in K562 cells. [provided by RefSeq, Feb 2023]
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Genomic context

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Location:
Xp11.21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (55023757..55030982)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (54316883..54324108)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (55050190..55057415)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chrX:54962395-54962556 Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:54977103-54977603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20865 Neighboring gene Sharpr-MPRA regulatory regions 2439 and 5762 Neighboring gene ALAS2 intronic erythroid enhancer Neighboring gene apurinic/apyrimidinic endodeoxyribonuclease 2 Neighboring gene 5'-aminolevulinate synthase 2 Neighboring gene PAGE family member 2B Neighboring gene HDGFL3 pseudogene 1 Neighboring gene PAGE family member 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. Transcriptional regulation of the human erythroid 5-aminolevulinate synthase gene. Identification of promoter elements and role of regulatory proteins. Surinya KH, et al. J Biol Chem, 1997 Oct 17. PMID 9334239
  2. Regulation of erythroid 5-aminolevulinate synthase expression during erythropoiesis. Sadlon TJ, et al. Int J Biochem Cell Biol, 1999 Oct. PMID 10582344
  3. Identification and characterization of a conserved erythroid-specific enhancer located in intron 8 of the human 5-aminolevulinate synthase 2 gene. Surinya KH, et al. J Biol Chem, 1998 Jul 3. PMID 9642238
  4. Insight into GATA1 transcriptional activity through interrogation of cis elements disrupted in human erythroid disorders. Wakabayashi A, et al. Proc Natl Acad Sci U S A, 2016 Apr 19. PMID 27044088, Free PMC Article
  5. Genome-wide enhancer maps link risk variants to disease genes. Nasser J, et al. Nature, 2021 May. PMID 33828297, 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

  • CRISPRi-validated ALAS2 cis-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_051542.1 

    Range
    101..7326
    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
    55023757..55030982
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    54316883..54324108
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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