Human Gene TCF7L2 (uc001lae.4)
  Description: Homo sapiens transcription factor 7-like 2 (T-cell specific, HMG-box) (TCF7L2), transcript variant 1, mRNA.
RefSeq Summary (NM_001146274): This gene encodes a high mobility group (HMG) box-containing transcription factor that plays a key role in the Wnt signaling pathway. The protein has been implicated in blood glucose homeostasis. Genetic variants of this gene are associated with increased risk of type 2 diabetes. Several transcript variants encoding multiple different isoforms have been found for this gene.[provided by RefSeq, Oct 2010].
Transcript (Including UTRs)
   Position: hg19 chr10:114,710,009-114,927,436 Size: 217,428 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr10:114,710,516-114,925,731 Size: 215,216 Coding Exon Count: 14 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:114,710,009-114,927,436)mRNA (may differ from genome)Protein (602 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TCF7L2
CDC HuGE Published Literature: TCF7L2
Positive Disease Associations: Blood Pressure Determination , body mass cholesterol, HDL diabetes, type 2 glucose insulin metabolic syndrome triglycerides , body mass insulin , clinicopathological characteristics of hepatocellular carcinoma , coronary artery disease , Coronary Disease , Diabetes mellitus type II|Diabetes Mellitus, Type 2 , Diabetes mellitus type II|Diabetes Mellitus, Type 2|Insulin Resistance , Diabetes Mellitus, Type 2 , diabetes, gestational , diabetes, type 2 , diabetes, type 2 glucose insulin , fasting glucose-related traits , Glucose Tolerance Test , Hemoglobin A, Glycosylated , Posttransplantation diabetes mellitus (PTDM) , two-hour glucose challenge , type 2 diabetes , type 2 diabetes and other traits
Related Studies:
  1. Blood Pressure Determination
    , , . [PubMed 0]
  2. body mass cholesterol, HDL diabetes, type 2 glucose insulin metabolic syndrome triglycerides
    Melzer, D. et al. 2006, Effects of the diabetes linked TCF7L2 polymorphism in a representative older population, BMC Med 2006 4(1) 34. [PubMed 17181866]
    The TCF7L2 rs7903146 polymorphism is associated with lower insulin levels, smaller waist circumference, and lower risk lipid profiles in the general elderly population.
  3. body mass insulin
    Munoz, J. et al. 2006, Polymorphism in the Transcription Factor 7-Like 2 (TCF7L2) Gene Is Associated With Reduced Insulin Secretion in Nondiabetic Women, Diabetes 2006 55(12) 3630-4. [PubMed 17130514]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TCF7L2
Diseases sorted by gene-association score: diabetes mellitus, noninsulin-dependent* (140), colorectal cancer (15), tropical calcific pancreatitis (7), gestational diabetes (6), acute insulin response (6), prediabetes syndrome (5), breast cancer (3), prostate cancer (2), glucose metabolism disease (1)
* = 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: 17.00 RPKM in Breast - Mammary Tissue
Total median expression: 393.87 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 -116.33507-0.229 Picture PostScript Text
3' UTR -400.911705-0.235 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
  Pfam Domains:
PF00505 - HMG (high mobility group) box
PF08347 - N-terminal CTNNB1 binding
PF09011 - HMG-box domain

SCOP Domains:
47095 - HMG-box

ModBase Predicted Comparative 3D Structure on Q9NQB0-7
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     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK225809 - Homo sapiens mRNA for Splice isoform 8 of Q9NQB0 variant, clone: FCC130A07.
FJ010174 - Homo sapiens TCF7L2 isoform pFC8A_TCF7L2_ex1-11-13-14 mRNA, complete cds, alternatively spliced.
Y11306 - Homo sapiens mRNA for hTCF-4.
AK315243 - Homo sapiens cDNA, FLJ96245.
FJ010168 - Homo sapiens TCF7L2 isoform pFC8A_TCF7L2_H7_ex1-11-13-13b mRNA, complete cds, alternatively spliced.
FJ010169 - Homo sapiens TCF7L2 isoform pFC8A_TCF7L2_B1_ex1-11-12-13-13b mRNA, complete cds, alternatively spliced.
FJ010172 - Homo sapiens TCF7L2 isoform pFC8A_TCF7L2_B8_ex1-11-14 mRNA, complete cds, alternatively spliced.
FJ010170 - Homo sapiens TCF7L2 isoform pFC8A_TCF7L2_ex1-11-12-14 mRNA, complete cds, alternatively spliced.
FJ010166 - Homo sapiens TCF7L2 isoform pFC8A_TCF7L2_A3,ex1-12,13,13a mRNA, complete cds, alternatively spliced.
FJ010167 - Homo sapiens TCF7L2 isoform pFC8A_TCF7L2_D4,ex1-11-13a-14 mRNA, complete cds, alternatively spliced.
BC032656 - Homo sapiens transcription factor 7-like 2 (T-cell specific, HMG-box), mRNA (cDNA clone MGC:44932 IMAGE:5533185), complete cds.
FJ010171 - Homo sapiens TCF7L2 isoform pFC8A_TCF7L2_B4_ex1-no4-11-14 mRNA, complete cds, alternatively spliced.
AK299295 - Homo sapiens cDNA FLJ60833 complete cds, highly similar to Transcription factor 7-like 2.
KJ892257 - Synthetic construct Homo sapiens clone ccsbBroadEn_01651 TCF7L2 gene, encodes complete protein.
AB451266 - Homo sapiens TCF7L2 mRNA for transcription factor 7-like 2, complete cds, clone: FLJ08086AAAN.
AB440195 - Homo sapiens TCF7L2 mRNA for transcription factor 7-like 2 isoform, complete cds.
CR536574 - Homo sapiens full open reading frame cDNA clone RZPDo834H0722D for gene TCF7L2, transcription factor 7-like 2 (T-cell specific, HMG-box); complete cds, incl. stopcodon.
HM352838 - Homo sapiens T-cell factor-4 variant F (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352839 - Homo sapiens T-cell factor-4 variant K (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352840 - Homo sapiens T-cell factor-4 variant D (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352841 - Homo sapiens T-cell factor-4 variant H (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352842 - Homo sapiens T-cell factor-4 variant B (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352843 - Homo sapiens T-cell factor-4 variant C (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352844 - Homo sapiens T-cell factor-4 variant I (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352845 - Homo sapiens T-cell factor-4 variant X2 (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352846 - Homo sapiens T-cell factor-4 variant G (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352847 - Homo sapiens T-cell factor-4 variant J (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352848 - Homo sapiens T-cell factor-4 variant E (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352849 - Homo sapiens T-cell factor-4 variant A (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352850 - Homo sapiens T-cell factor-4 variant M (TCF7L2) mRNA, complete cds, alternatively spliced.
HM352851 - Homo sapiens T-cell factor-4 variant L (TCF7L2) mRNA, complete cds, alternatively spliced.
MF772717 - Homo sapiens transcription factor 7 like 2 isoform E1 (TCF7L2) mRNA, complete cds.
MF772718 - Homo sapiens transcription factor 7 like 2 isoform E4 (TCF7L2) mRNA, complete cds.
BX648364 - Homo sapiens mRNA; cDNA DKFZp686K06191 (from clone DKFZp686K06191).
FJ010164 - Homo sapiens TCF7L2 isoform pFC8A_TCF7L2_D5_ex3-11,12,13a,14 mRNA, complete cds, alternatively spliced.
FJ010165 - Homo sapiens TCF7L2 isoform pFC8A_TCF7L2_D5_ex3,4a-11,12,13a,14 mRNA, complete cds, alternatively spliced.
FJ010173 - Homo sapiens TCF7L2 isoform pFC8A_TCF7L2_H2_ex3-11-12-13-14 mRNA, complete cds, alternatively spliced.
AK301483 - Homo sapiens cDNA FLJ54563 complete cds, highly similar to Transcription factor 7-like 2.
JD391258 - Sequence 372282 from Patent EP1572962.
JD402306 - Sequence 383330 from Patent EP1572962.
JD390508 - Sequence 371532 from Patent EP1572962.
JD415834 - Sequence 396858 from Patent EP1572962.
JD298789 - Sequence 279813 from Patent EP1572962.
JD399025 - Sequence 380049 from Patent EP1572962.
JD163189 - Sequence 144213 from Patent EP1572962.
LF211376 - JP 2014500723-A/18879: Polycomb-Associated Non-Coding RNAs.
LF345953 - JP 2014500723-A/153456: Polycomb-Associated Non-Coding RNAs.
LF383497 - JP 2014500723-A/191000: Polycomb-Associated Non-Coding RNAs.
MA581530 - JP 2018138019-A/153456: Polycomb-Associated Non-Coding RNAs.
MA619074 - JP 2018138019-A/191000: Polycomb-Associated Non-Coding RNAs.
MA446953 - JP 2018138019-A/18879: Polycomb-Associated Non-Coding RNAs.
AK316111 - Homo sapiens cDNA, FLJ79010 complete cds, highly similar to Transcription factor 7-like 2.
AK303684 - Homo sapiens cDNA FLJ59810 complete cds, highly similar to Transcription factor 7-like 2.
AK296305 - Homo sapiens cDNA FLJ59705 complete cds, highly similar to Transcription factor 7-like 2.
AK074705 - Homo sapiens cDNA FLJ90224 fis, clone NT2RM1000789, highly similar to Mus musculus transcription factor 7-like 2, T-cell specific, HMG-box (Tcf7l2), mRNA.
AB034691 - Homo sapiens TCF-4B mRNA for TCF-4 splice form B, partial cds.
JD206620 - Sequence 187644 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04310 - Wnt signaling pathway
hsa04520 - Adherens junction
hsa04916 - Melanogenesis
hsa05200 - Pathways in cancer
hsa05210 - Colorectal cancer
hsa05213 - Endometrial cancer
hsa05215 - Prostate cancer
hsa05216 - Thyroid cancer
hsa05217 - Basal cell carcinoma
hsa05221 - Acute myeloid leukemia
hsa05412 - Arrhythmogenic right ventricular cardiomyopathy (ARVC)

Reactome (by CSHL, EBI, and GO)

Protein Q9NQB0 (Reactome details) participates in the following event(s):

R-HSA-8944352 TCF/LEF binds WNT promoters
R-HSA-5334050 TCF7L2/TCF7L1 bind CTBP1 to repress WNT target genes
R-HSA-3364014 Recruitment of SET1 methyltransferase complex
R-HSA-201712 Beta-catenin:TCF associates with BCL9 and PYGO
R-HSA-3322422 Beta-catenin recruits SMARCA4
R-HSA-3322424 Beta-catenin recruits CDC73 and LEO1
R-HSA-3322427 Beta-catenin recruits CBP/p300
R-HSA-3451153 Beta-catenin recruits TRRAP/KAT5 HAT components
R-HSA-5665608 TCF:Beta-catenin binds SOX proteins
R-HSA-8944362 TCF/LEF:CTNNB1 bind canonical WNT target promoters
R-HSA-3299569 Beta-catenin displaces TLE:HDAC1 from TCF/LEF
R-HSA-8944349 TLE tetramers bind TCF/LEF at WNT promoters
R-HSA-4411383 NLK phosphorylates TCF/LEF
R-HSA-4411351 TCF/LEF:CTNNB1 bind the AXIN2 gene
R-HSA-8951442 CTNNB1:TCF7L2,LEF1 binds the CCND1 gene promoter
R-HSA-8951428 RUNX3 binds CTNNB1:TCF7L2,(LEF1,TCF7L1,TCF7)
R-HSA-4411367 TCF7L1/TCF7L2/LEF1:CTNNB1 bind the MYC gene
R-HSA-3364026 SET1 complex trimethylates H3K4 at the MYC gene
R-HSA-4641231 TLE recruits HDAC1 to WNT promoters
R-HSA-3451147 KAT5 HAT complex acetylates TCF4 gene at histone H4
R-HSA-4641265 Repression of WNT target genes
R-HSA-5339700 TCF7L2 mutants don't bind CTBP
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex
R-HSA-4086398 Ca2+ pathway
R-HSA-195253 Degradation of beta-catenin by the destruction complex
R-HSA-4411364 Binding of TCF/LEF:CTNNB1 to target gene promoters
R-HSA-8951430 RUNX3 regulates WNT signaling
R-HSA-4791275 Signaling by WNT in cancer
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-3858494 Beta-catenin independent WNT signaling
R-HSA-195721 Signaling by WNT
R-HSA-8878159 Transcriptional regulation by RUNX3
R-HSA-5663202 Diseases of signal transduction
R-HSA-162582 Signal Transduction
R-HSA-212436 Generic Transcription Pathway
R-HSA-1643685 Disease
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001146274, NP_001139746, Q9NQB0-7, TCF4
UCSC ID: uc001lae.4
RefSeq Accession: NM_001146274
Protein: Q9NQB0-7, splice isoform of Q9NQB0 CCDS: CCDS53577.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001146274.1
exon count: 14CDS single in 3' UTR: no RNA size: 4022
ORF size: 1809CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3437.00frame shift in genome: no % Coverage: 99.98
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.