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LOC109286563 TBX21 promoter region [ Homo sapiens (human) ]

Gene ID: 109286563, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109286563
Gene description
TBX21 promoter region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: promoter, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region encompasses the promoter of the T-box 21 gene. This promoter is stimulated by early growth response 1 and interleukins, and downregulated by transforming growth factor beta through SMAD family members. Naturally occurring polymorphisms in this sequence may affect binding of transcriptional regulators, which may influence promoter activity and susceptibility to immune disorders. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to 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, May 2023]
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Genomic context

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Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (47731244..47733594)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48593054..48595404)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (45808610..45810609)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12314 Neighboring gene karyopherin subunit beta 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:45771282-45771962 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45771963-45772642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45772643-45773323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8638 Neighboring gene TBK1 binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45791473-45791974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45791975-45792474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12316 Neighboring gene T-box transcription factor 21 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45855331-45855844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45866576-45867378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45867379-45868179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45885766-45886266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45886267-45886767 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:45899123-45899338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12317 Neighboring gene oxysterol binding protein like 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45907489-45908320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45908321-45909150 Neighboring gene mitochondrial ribosomal protein L10

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. Pro- and antiinflammatory cytokine signaling: reciprocal antagonism regulates interferon-gamma production by human natural killer cells. Yu J, et al. Immunity, 2006 May. PMID 16713975
  2. TBX21-1993T/C (rs4794067) polymorphism is associated with increased risk of chronic periodontitis and increased T-bet expression in periodontal lesions, but does not significantly impact the IFN-g transcriptional level or the pattern of periodontophatic bacterial infection. Cavalla F, et al. Virulence, 2015. PMID 25832120, Free PMC Article
  3. Association between the genetic variations within TBX21 gene promoter and the clinicopathological characteristics of esophageal squamous cell carcinoma in a high-risk Chinese population. Li H, et al. Tumour Biol, 2015 May. PMID 25577251
  4. The TBX21 transcription factor T-1993C polymorphism is associated with decreased IFN-γ and IL-4 production by primary human lymphocytes. Fyall KM, et al. Hum Immunol, 2012 Jun. PMID 22521571, Free PMC Article
  5. Association between gastric cancer and -1993 polymorphism of TBX21 gene. Zhang LH, et al. World J Gastroenterol, 2012 Mar 14. PMID 22416188, Free PMC Article

See all (14) 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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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 8639

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_052584.2 

    Range
    101..2451
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    47731244..47733594
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    48593054..48595404
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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