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

Gene ID: 107303343, updated on 17-Sep-2024

Summary

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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
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Genomic context

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See LOC107303343 in Genome Data Viewer
Location:
20q13.12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (44629004..44652471)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (46364776..46388246)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (43257645..43281112)

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

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Functional analysis of the human adenosine deaminase gene thymic regulatory region and its ability to generate position-independent transgene expression. Aronow BJ, et al. Mol Cell Biol, 1992 Sep. PMID 1508212, Free PMC Article
  2. Winner of the Theodore E. Woodward Award: c-Myb and the coordinate regulation of thymic genes. Hutton JJ, et al. Trans Am Clin Climatol Assoc, 1996. PMID 8725565, Free PMC Article
  3. Sp1 is essential for both enhancer-mediated and basal activation of the TATA-less human adenosine deaminase promoter. Dusing MR, et al. Nucleic Acids Res, 1994 Feb 25. PMID 8127716, Free PMC Article
  4. An enhancer LEF-1/TCF-1 site is essential for insertion site-independent transgene expression in thymus. Haynes TL, et al. Nucleic Acids Res, 1996 Dec 15. PMID 9016677, Free PMC Article
  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

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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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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)

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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_046759.2 

    Range
    101..23568
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
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    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

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