Human Gene TBX21 (uc002ilv.1) Description and Page Index
  Description: Homo sapiens T-box 21 (TBX21), mRNA.
RefSeq Summary (NM_013351): This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. This gene is the human ortholog of mouse Tbx21/Tbet gene. Studies in mouse show that Tbx21 protein is a Th1 cell-specific transcription factor that controls the expression of the hallmark Th1 cytokine, interferon-gamma (IFNG). Expression of the human ortholog also correlates with IFNG expression in Th1 and natural killer cells, suggesting a role for this gene in initiating Th1 lineage development from naive Th precursor cells. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AF093098.1, BC039739.2 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000177694.2/ ENSP00000177694.1 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr17:45,810,610-45,823,485 Size: 12,876 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr17:45,810,821-45,822,732 Size: 11,912 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:45,810,610-45,823,485)mRNA (may differ from genome)Protein (535 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: TBX21_HUMAN
DESCRIPTION: RecName: Full=T-box transcription factor TBX21; Short=T-box protein 21; AltName: Full=T-cell-specific T-box transcription factor T-bet; AltName: Full=Transcription factor TBLYM;
FUNCTION: Transcription factor that controls the expression of the TH1 cytokine, interferon-gamma. Initiates TH1 lineage development from naive TH precursor cells both by activating TH1 genetic programs and by repressing the opposing TH2 programs.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: T-cell specific.
DISEASE: Genetic variations in TBX21 are associated with susceptibility to asthma with nasal polyps and aspirin intolerance (ANPAI) [MIM:208550]. A condition consisting of asthma, aspirin sensitivity and nasal polyposis. Nasal polyposis is due to chronic inflammation of the paranasal sinus mucosa, leading to protrusion of edematous polyps into the nasal cavities.
SIMILARITY: Contains 1 T-box DNA-binding domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TBX21
CDC HuGE Published Literature: TBX21
Positive Disease Associations: asthma , hepatitis B
Related Studies:
  1. asthma
    Raby, B. A. et al. 2005, T-Bet Polymorphisms are Associated with Asthma and Airway Hyperresponsiveness., American journal of respiratory and critical care medicine. 2006 Jan;173(1):64-70. [PubMed 16179640]
    These data suggest that T-bet variation contributes to airway responsiveness in asthma.
  2. asthma
    Akahoshi, M. et al. 2005, Functional promoter polymorphism in the TBX21 gene associated with aspirin-induced asthma., Human genetics. 2005 Jun;117(1):16-26. [PubMed 15806396]
    Thus, in addition to the antigen-driven excess Th2 response, increased T-bet (and subsequent IFN-gamma) production in human airways of individuals with the -1993T-->C polymorphism could contribute to the development of certain asthma-related phenotypes, such as AIA.
  3. hepatitis B
    Cao, B. et al. 2007, Association analysis of hepatitis virus B infection with haplotypes of the TBX21 gene promoter region in the Chinese population, Clin Chem Lab Med 2007 45(3) 333-8. [PubMed 17378728]
    Based on our findings, it seems that genetic variations of allele -1499 and haplotype D (--/AC) within the TBX21 promoter region contribute to susceptibility to HBV infection in the Chinese population.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TBX21
Diseases sorted by gene-association score: asthma, aspirin-induced* (575), genital herpes (13), acute necrotizing encephalitis (11), heart sarcoma (7), erythema elevatum diutinum (6), asthma (5), ecthyma (4), aplastic anemia (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.88 RPKM in Spleen
Total median expression: 35.89 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -107.00211-0.507 Picture PostScript Text
3' UTR -270.10753-0.359 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008967 - p53-like_TF_DNA-bd
IPR001699 - TF_T-box
IPR018186 - TF_T-box_CS

Pfam Domains:
PF00907 - T-box

SCOP Domains:
49417 - p53-like transcription factors

ModBase Predicted Comparative 3D Structure on Q9UL17
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0009615 response to virus
GO:0010628 positive regulation of gene expression
GO:0030217 T cell differentiation
GO:0032703 negative regulation of interleukin-2 production
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045580 regulation of T cell differentiation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0048304 positive regulation of isotype switching to IgG isotypes
GO:0050776 regulation of immune response
GO:0071310 cellular response to organic substance
GO:0072676 lymphocyte migration
GO:2000320 negative regulation of T-helper 17 cell differentiation
GO:2000329 negative regulation of T-helper 17 cell lineage commitment
GO:2000552 negative regulation of T-helper 2 cell cytokine production

Cellular Component:
GO:0005634 nucleus
GO:0043025 neuronal cell body


-  Descriptions from all associated GenBank mRNAs
  AF093098 - Homo sapiens transcription factor TBLYM (TBLYM) mRNA, complete cds.
AK223634 - Homo sapiens mRNA for T-box 21 variant, clone: FCC135F08.
BC039739 - Homo sapiens T-box 21, mRNA (cDNA clone MGC:47672 IMAGE:6067371), complete cds.
AF241243 - Homo sapiens T-cell-specific T-box transcription factor T-bet mRNA, complete cds.
JD469244 - Sequence 450268 from Patent EP1572962.
AB590854 - Synthetic construct DNA, clone: pFN21AB7819, Homo sapiens TBX21 gene for T-box 21, without stop codon, in Flexi system.
JD125049 - Sequence 106073 from Patent EP1572962.
JD464477 - Sequence 445501 from Patent EP1572962.
JD077702 - Sequence 58726 from Patent EP1572962.
JD068573 - Sequence 49597 from Patent EP1572962.
JD324761 - Sequence 305785 from Patent EP1572962.
JD250745 - Sequence 231769 from Patent EP1572962.
JD051803 - Sequence 32827 from Patent EP1572962.
MP202746 - Sequence 57 from Patent WO2019090263.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_013351, NP_037483, Q9UL17, TBET, TBLYM, TBX21_HUMAN
UCSC ID: uc002ilv.1
RefSeq Accession: NM_013351
Protein: Q9UL17 (aka TBX21_HUMAN or TX21_HUMAN)
CCDS: CCDS11514.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_013351.1
exon count: 6CDS single in 3' UTR: no RNA size: 2589
ORF size: 1608CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3416.00frame shift in genome: no % Coverage: 99.34
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.