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LOC112679198 ABO +5.8 intron 1 enhancer [ Homo sapiens (human) ]

Gene ID: 112679198, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112679198
Gene description
ABO +5.8 intron 1 enhancer
Gene type
biological region
Feature type(s)
protein_bind
regulatory: DNase_I_hypersensitive_site, enhancer, 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 is located in the first intron of the ABO (ABO, alpha 1-3-N-acetylgalactosaminyltransferase and alpha 1-3-galactosyltransferase) blood group gene on the q arm of chromosome 9. It includes a DNase I hypersensitive site in several cell types. This region was shown to function as an ABO enhancer in transfected K562 erythroleukemia cells, with activity dependent on binding sites for GATA and RUNX1 transcription factors. This enhancer region is polymorphic in different ABO haplotypes, where some alleles include a deletion of the entire region, while others include point mutations, some of which affect known protein-binding sites and can reduce activity of the ABO promoter. Polymorphisms within this region were shown to be associated with severe coronavirus disease 2019 (COVID-19). [provided by RefSeq, Aug 2020]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is involved in host gene regulation.
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (133267998..133270594)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (145481870..145484465)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 (PATCHES) NW_003315925.1 (94092..96688)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136102720-136103675 Neighboring gene uncharacterized LOC124902294 Neighboring gene lipocalin 1 pseudogene 1 Neighboring gene ABO +36.0 downstream enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136114423-136115032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136115033-136115642 Neighboring gene ABO 3' regulatory region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:136130804-136131336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136133484-136134469 Neighboring gene ABO, alpha 1-3-N-acetylgalactosaminyltransferase and alpha 1-3-galactosyltransferase Neighboring gene ABO promoter region Neighboring gene ABO upstream enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:136179717-136180405 Neighboring gene lipocalin 1 pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:136202031-136203002 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:136203003-136203973 Neighboring gene surfeit 6

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. ABO alleles are linked with haplotypes of an erythroid cell-specific regulatory element in intron 1 with a few exceptions attributable to genetic recombination. Nakajima T, et al. Vox Sang, 2016 Jan. PMID 26178450
  2. A novel mutation of the GATA site in the erythroid cell-specific regulatory element of the ABO gene in a blood donor with the Am B phenotype. Oda A, et al. Vox Sang, 2015 May. PMID 25557060
  3. Blood group B gene is barely expressed in in vitro erythroid culture of Bm-derived CD34+ cells without an erythroid cell-specific regulatory element. Sano R, et al. Vox Sang, 2015 Apr. PMID 25523606
  4. A 3.0-kb deletion including an erythroid cell-specific regulatory element in intron 1 of the ABO blood group gene in an individual with the Bm phenotype. Sano R, et al. Vox Sang, 2015 Apr. PMID 25523382
  5. The B allele with a 5·8 kb deletion in intron 1 of the ABO gene is the major allele in Japanese individuals with B(m) and A(1) B(m) phenotypes. Ogasawara K, et al. Vox Sang, 2018 May. PMID 29473176

See all (12) citations in PubMed

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_060715.1 

    Range
    101..2697
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    133267998..133270594
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646201.1 Reference GRCh38.p14 PATCHES

    Range
    94092..96688
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    145481870..145484465
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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