U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC107303343 adenosine deaminase intronic regulatory elements [ Homo sapiens (human) ]

Gene ID: 107303343, updated on 14-Mar-2024

Summary

Go to the top of the page Help
Gene symbol
LOC107303343
Gene description
adenosine deaminase intronic regulatory elements
Gene type
biological region
Feature type(s)
protein_bind
regulatory: DNase_I_hypersensitive_site, enhancer, locus_control_region, 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 represents regulatory elements located in two 5' introns of the adenosine deaminase (ADA) gene. These elements control tissue-specific and developmental expression of the ADA gene, and are characterized by arrays of DNase I hypersensitive sites. They include an enhancer and locus control region (LCR) that regulates ADA expression in the thymus, and an independent enhancer that regulates ADA expression in the duodenum. Various transcription factors can bind to these elements and are necessary for their function. Eight subregions were validated as active enhancers by ChIP-STARR-seq in human embryonic stem cells, where all are marked by the H3K4me1 histone modification, five are additionally marked by H3K27ac, and one is additionally associated with the NANOG transcription factor. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) K562 erythroleukemia cells. This locus also includes seven accessible chromatin subregions, five of which were validated as enhancers and two as silencers, based on their ability to activate or repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, Jun 2023]
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
20q13.12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (44629004..44652471)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (46364776..46388246)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (43257645..43280208)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:43124829-43126028 Neighboring gene serine incorporator 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:43149922-43150474 Neighboring gene Sharpr-MPRA regulatory region 7879 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:43152936-43153812 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:43154689-43155564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:43160105-43160605 Neighboring gene cAMP-dependent protein kinase inhibitor gamma Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:43226219-43226966 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:43229479-43229980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:43237694-43238268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17933 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:43246415-43247142 Neighboring gene proximal ADA Alu-mediated recombination region Neighboring gene adenosine deaminase Neighboring gene distal ADA Alu-mediated recombination region Neighboring gene long intergenic non-protein coding RNA 1260 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:43299119-43299620 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:43299621-43300120 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:43306608-43307108 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:43307109-43307609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17940 Neighboring gene uncharacterized LOC124904911 Neighboring gene Sharpr-MPRA regulatory region 14821 Neighboring gene KCNK15 and WISP2 antisense RNA 1

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Temporal regulation of enhancer function in intestinal epithelium: a role for Onecut factors. Maier EA, et al. J Biol Chem, 2006 Oct 27. PMID 16950765
  2. Transcriptional regulatory elements in the human genome. Maston GA, et al. Annu Rev Genomics Hum Genet, 2006. PMID 16719718
  3. Pdx-1 is required for activation in vivo from a duodenum-specific enhancer. Dusing MR, et al. J Biol Chem, 2001 Apr 27. PMID 11278481
  4. A duodenum-specific enhancer regulates expression along three axes in the small intestine. Dusing MR, et al. Am J Physiol Gastrointest Liver Physiol, 2000 Nov. PMID 11053006
  5. Regulation of duodenal specific expression of the human adenosine deaminase gene. Dusing MR, et al. J Biol Chem, 1997 Oct 17. PMID 9334245

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Homology

Other Names

  • ADA duodenal enhancer
  • ADA locus control region
  • ADA thymic enhancer
  • ATAC-STARR-seq lymphoblastoid active region 17934
  • ATAC-STARR-seq lymphoblastoid active region 17935
  • ATAC-STARR-seq lymphoblastoid active region 17936
  • ATAC-STARR-seq lymphoblastoid active region 17937
  • ATAC-STARR-seq lymphoblastoid active region 17938
  • ATAC-STARR-seq lymphoblastoid silent region 12943
  • ATAC-STARR-seq lymphoblastoid silent region 12944
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:43271018-43271607
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:43271608-43272198
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:43272199-43272788
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:43274795-43275310
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:43280129-43281112
  • H3K4me1 hESC enhancer GRCh37_chr20:43257882-43258632
  • H3K4me1 hESC enhancer GRCh37_chr20:43276699-43277199
  • NANOG-H3K4me1 hESC enhancer GRCh37_chr20:43258633-43259382
  • ReSE screen-validated silencer GRCh37_chr20:43276508-43276676
  • adenosine deaminase LCR

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_046759.2 

    Range
    101..23568
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    44629004..44652471
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    46364776..46388246
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases