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LOC109286564 TBX22 P0 promoter [ Homo sapiens (human) ]

Gene ID: 109286564, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109286564
Gene description
TBX22 P0 promoter
Gene type
biological region
Feature type(s)
protein_bind
regulatory: enhancer, promoter
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region represents the proximal P0 promoter of the T-box 22 gene. A naturally occurring polymorphism in this sequence affects binding of ETS proto-oncogene and is associated with cleft palate. A subregion was also validated as an enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (80014145..80014843)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (78446414..78447112)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (79270087..79270342)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene CORO1C pseudogene 1 Neighboring gene uncharacterized LOC105373282 Neighboring gene NANOG hESC enhancer GRCh37_chrX:78856708-78857363 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:79277949-79278449 Neighboring gene T-box transcription factor 22 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:79471575-79472774 Neighboring gene charged multivesicular body protein 1B2, pseudogene Neighboring gene Sharpr-MPRA regulatory region 5203 Neighboring gene terminal nucleotidyltransferase 5D

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. Two promoter polymorphisms in TBX22 are associated with the risk of NSCLP in Indian women. Gurramkonda VB, et al. Clin Dysmorphol, 2015 Oct. PMID 25918826
  2. A functional haplotype variant in the TBX22 promoter is associated with cleft palate and ankyloglossia. Pauws E, et al. J Med Genet, 2009 Aug. PMID 19648124
  3. TBX22 missense mutations found in patients with X-linked cleft palate affect DNA binding, sumoylation, and transcriptional repression. Andreou AM, et al. Am J Hum Genet, 2007 Oct. PMID 17846996, Free PMC Article
  4. Loss-of-function mutation in the X-linked TBX22 promoter disrupts an ETS-1 binding site and leads to cleft palate. Fu X, et al. Hum Genet, 2015 Feb. PMID 25373698
  5. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:79269644-79270208

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_052585.2 

    Range
    101..799
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    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
    80014145..80014843
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187635.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    82240..82938 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    78446414..78447112
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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