Human Gene TBX18 (uc003pkl.2) Description and Page Index
  Description: Homo sapiens T-box 18 (TBX18), mRNA.
RefSeq Summary (NM_001080508): This genes codes for a member of an evolutionarily conserved family of transcription factors that plays a crucial role in embryonic development. The family is characterized by the presence of the DNA-binding T-box domain and is divided into five sub-families based on sequence conservation in this domain. The encoded protein belongs to the vertebrate specific Tbx1 sub-family. The protein acts as a transcriptional repressor by antagonizing transcriptional activators in the T-box family. The protein forms homo- or heterodimers with other transcription factors of the T-box family or other transcription factors. [provided by RefSeq, Nov 2012]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. 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 :: BC157841.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2467147 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000369663.10/ ENSP00000358677.4 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr6:85,442,216-85,473,954 Size: 31,739 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr6:85,446,403-85,473,899 Size: 27,497 Coding Exon Count: 8 

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 (chr6:85,442,216-85,473,954)mRNA (may differ from genome)Protein (607 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: TBX18_HUMAN
DESCRIPTION: RecName: Full=T-box transcription factor TBX18; Short=T-box protein 18;
FUNCTION: Probable transcriptional regulator involved in developmental processes.
SUBCELLULAR LOCATION: Nucleus (Potential).
SIMILARITY: Contains 1 T-box DNA-binding domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TBX18
CDC HuGE Published Literature: TBX18
Positive Disease Associations: Body Weights and Measures , Calcium , Cholesterol , Cholesterol, LDL , Coronary Artery Disease , Forced Vital Capacity , Hand Strength , Hip , Mental Competency , Occipital Lobe , Triglycerides
Related Studies:
  1. Body Weights and Measures
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  2. Body Weights and Measures
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. Calcium
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TBX18
Diseases sorted by gene-association score: congenital anomalies of kidney and urinary tract 2* (1580), bilateral multicystic dysplastic kidney* (400), congenital anomalies of kidney and urinary tract (17), posterior urethral valves (13), ulnar-mammary syndrome (7), sinoatrial node disease (6)
* = 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: 15.59 RPKM in Artery - Tibial
Total median expression: 88.60 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 -18.6055-0.338 Picture PostScript Text
3' UTR -1026.704187-0.245 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 O95935
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000976 transcription regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001106 RNA polymerase II transcription corepressor activity
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0042803 protein homodimerization activity
GO:0046982 protein heterodimerization activity

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:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0060829 negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation
GO:0072001 renal system development
GO:1903507 negative regulation of nucleic acid-templated transcription

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC040697 - Homo sapiens T-box 18, mRNA (cDNA clone IMAGE:6023106), partial cds.
BC157841 - Homo sapiens T-box 18, mRNA (cDNA clone MGC:189736 IMAGE:9057060), complete cds.
BC132715 - Homo sapiens T-box 18, mRNA (cDNA clone MGC:164346 IMAGE:40146737), complete cds.
HQ258462 - Synthetic construct Homo sapiens clone IMAGE:100072891 T-box 18 (TBX18) gene, encodes complete protein.
KJ897965 - Synthetic construct Homo sapiens clone ccsbBroadEn_07359 TBX18 gene, encodes complete protein.
AK310179 - Homo sapiens cDNA, FLJ17221.
AJ010278 - Homo sapiens mRNA for TBX18 protein, partial.
AK308860 - Homo sapiens cDNA, FLJ98901.
JD141141 - Sequence 122165 from Patent EP1572962.
JD213635 - Sequence 194659 from Patent EP1572962.
JD281515 - Sequence 262539 from Patent EP1572962.
JD480703 - Sequence 461727 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A2RU13, NM_001080508, NP_001073977, O95935, Q7Z6U4, Q9UJI6, TBX18_HUMAN, uc003pkl.1
UCSC ID: uc003pkl.2
RefSeq Accession: NM_001080508
Protein: O95935 (aka TBX18_HUMAN or TX18_HUMAN)
CCDS: CCDS34495.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001080508.2
exon count: 8CDS single in 3' UTR: no RNA size: 6068
ORF size: 1824CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3830.50frame shift in genome: no % Coverage: 99.97
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.