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LOC112639999 ABO 3' regulatory region [ Homo sapiens (human) ]

Gene ID: 112639999, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112639999
Gene description
ABO 3' regulatory region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: DNase_I_hypersensitive_site, 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 region is located at the 3' end of the ABO (ABO, alpha 1-3-N-acetylgalactosaminyltransferase and alpha 1-3-galactosyltransferase) gene on the q arm of chromosome 9. It includes a DNase I hypersensitive site in multiple cell types. A sub-region was shown to function as an ABO enhancer in transfected KATO III gastric cancer cells, with activity dependent on two binding sites for the epithelial transcription factor, Elf5. This genomic region also includes an adjacent sub-region that was shown to negatively regulate the ABO promoter in both KATO III gastric cancer and K562 erythroleukemia cells. [provided by RefSeq, Nov 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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See LOC112639999 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (133251819..133254521)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (145465402..145468104)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (136127206..136129908)

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 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 +5.8 intron 1 enhancer 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. The 3' flanking region of the human ABO histo-blood group gene is involved in negative regulation of gene expression. Sano R, et al. Leg Med (Tokyo), 2011 Jan. PMID 21144789
  2. Epithelial Expression of Human ABO Blood Group Genes Is Dependent upon a Downstream Regulatory Element Functioning through an Epithelial Cell-specific Transcription Factor, Elf5. Sano R, et al. J Biol Chem, 2016 Oct 21. PMID 27587399, 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

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

  • ABO +22.6 downstream enhancer
  • ABO 3' repressive region

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_060714.1 

    Range
    101..2803
    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
    133251819..133254521
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646201.1 Reference GRCh38.p14 PATCHES

    Range
    77778..80480
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    145465402..145468104
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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