Human Gene TCF3 (uc002ltt.4)
  Description: Homo sapiens transcription factor 3 (TCF3), transcript variant 2, mRNA.
RefSeq Summary (NM_001136139): This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development. Deletion of this gene or diminished activity of the encoded protein may play a role in lymphoid malignancies. This gene is also involved in several chromosomal translocations that are associated with lymphoid malignancies including pre-B-cell acute lymphoblastic leukemia (t(1;19), with PBX1), childhood leukemia (t(19;19), with TFPT) and acute leukemia (t(12;19), with ZNF384). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Sep 2011].
Transcript (Including UTRs)
   Position: hg19 chr19:1,609,289-1,650,286 Size: 40,998 Total Exon Count: 19 Strand: -
Coding Region
   Position: hg19 chr19:1,611,706-1,650,247 Size: 38,542 Coding Exon Count: 18 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:1,609,289-1,650,286)mRNA (may differ from genome)Protein (651 aa)
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-  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.
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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


-  MalaCards Disease Associations
  MalaCards Gene Search: TCF3
Diseases sorted by gene-association score: agammaglobulinemia 8, autosomal dominant* (1019), agammaglobulinemia, non-bruton type* (202), leukemia, acute lymphoblastic 3* (111), childhood leukemia (34), lymphoblastic leukemia (23), agammaglobulinemia (9), acute leukemia (8), alveolar soft-part sarcoma (6), colorectal cancer (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: 44.07 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 495.10 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -15.1039-0.387 Picture PostScript Text
3' UTR -820.402083-0.394 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:
PF00010 - Helix-loop-helix DNA-binding domain

SCOP Domains:
47459 - HLH, helix-loop-helix DNA-binding domain

ModBase Predicted Comparative 3D Structure on P15923-2
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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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Descriptions from all associated GenBank mRNAs
  LF385513 - JP 2014500723-A/193016: Polycomb-Associated Non-Coding RNAs.
AK024806 - Homo sapiens cDNA: FLJ21153 fis, clone CAS09631, highly similar to HUMTFAA Human transcription factor (E2A) mRNA.
BC005166 - Homo sapiens transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47), mRNA (cDNA clone IMAGE:3534334), partial cds.
BC014680 - Homo sapiens transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47), mRNA (cDNA clone IMAGE:3864558), with apparent retained intron.
BC011665 - Homo sapiens transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47), mRNA (cDNA clone IMAGE:4110737), partial cds.
LP895383 - Sequence 247 from Patent EP3253886.
M31523 - Human transcription factor (E2A) mRNA, complete cds.
JD056660 - Sequence 37684 from Patent EP1572962.
JD246087 - Sequence 227111 from Patent EP1572962.
JD401418 - Sequence 382442 from Patent EP1572962.
JD360579 - Sequence 341603 from Patent EP1572962.
JD385632 - Sequence 366656 from Patent EP1572962.
X52078 - Human transcription factor (ITF-1) mRNA, 3' end.
JD124094 - Sequence 105118 from Patent EP1572962.
JD214439 - Sequence 195463 from Patent EP1572962.
JD237351 - Sequence 218375 from Patent EP1572962.
JD417237 - Sequence 398261 from Patent EP1572962.
JD226178 - Sequence 207202 from Patent EP1572962.
JD036997 - Sequence 18021 from Patent EP1572962.
JD536951 - Sequence 517975 from Patent EP1572962.
JD204098 - Sequence 185122 from Patent EP1572962.
JD426001 - Sequence 407025 from Patent EP1572962.
JD398100 - Sequence 379124 from Patent EP1572962.
JD390584 - Sequence 371608 from Patent EP1572962.
JD090402 - Sequence 71426 from Patent EP1572962.
JD376226 - Sequence 357250 from Patent EP1572962.
JD551503 - Sequence 532527 from Patent EP1572962.
JD528784 - Sequence 509808 from Patent EP1572962.
JD503576 - Sequence 484600 from Patent EP1572962.
JD077756 - Sequence 58780 from Patent EP1572962.
JD395984 - Sequence 377008 from Patent EP1572962.
JD205848 - Sequence 186872 from Patent EP1572962.
JD519795 - Sequence 500819 from Patent EP1572962.
JD317995 - Sequence 299019 from Patent EP1572962.
JD368963 - Sequence 349987 from Patent EP1572962.
JD365131 - Sequence 346155 from Patent EP1572962.
JD065698 - Sequence 46722 from Patent EP1572962.
JD388736 - Sequence 369760 from Patent EP1572962.
AK310998 - Homo sapiens cDNA, FLJ18040.
JD325269 - Sequence 306293 from Patent EP1572962.
JD231312 - Sequence 212336 from Patent EP1572962.
JD080793 - Sequence 61817 from Patent EP1572962.
JD126332 - Sequence 107356 from Patent EP1572962.
JD384585 - Sequence 365609 from Patent EP1572962.
JD219053 - Sequence 200077 from Patent EP1572962.
JD502482 - Sequence 483506 from Patent EP1572962.
M31222 - Human e12 protein (E2A) mRNA, complete cds.
M65214 - Human (HeLa) helix-loop-helix protein HE47 (E2A) mRNA, 3' end.
JD510113 - Sequence 491137 from Patent EP1572962.
BC110579 - Homo sapiens transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47), mRNA (cDNA clone MGC:129647 IMAGE:40007777), complete cds.
BC110580 - Homo sapiens transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47), mRNA (cDNA clone MGC:129648 IMAGE:40007779), complete cds.
M24405 - Homo sapiens (clone E12) kappa-E2-binding factor mRNA, 3' end.
KF303591 - Homo sapiens cell-line K562 transcription factor 3 variant 3 (TCF3) mRNA, complete cds.
KJ905326 - Synthetic construct Homo sapiens clone ccsbBroadEn_14857 TCF3-like gene, encodes complete protein.
AB385055 - Synthetic construct DNA, clone: pF1KB5152, Homo sapiens TCF3 gene for transcription factor E2-alpha, complete cds, without stop codon, in Flexi system.
M24404 - Homo sapiens (clone E47) kappa-E2-binding factor mRNA, partial cds.
AY311345 - Homo sapiens E2A/PBX1 fusion protein (E2A/PBX1 fusion) mRNA, partial cds; alternatively spliced.
EU155120 - Homo sapiens p120-E2A fusion (NOL1-TCF3 fusion) mRNA, partial sequence.
JD401067 - Sequence 382091 from Patent EP1572962.
MA621090 - JP 2018138019-A/193016: Polycomb-Associated Non-Coding RNAs.
MK158097 - Homo sapiens isolate 25595 E2A/HLF fusion protein mRNA, partial cds.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P15923 (Reactome details) participates in the following event(s):

R-HSA-448948 Phosphorylation of E proteins by p38 MAPK
R-HSA-448962 Heterodimerization of E proteins with Myod
R-HSA-448963 Interaction of MyoD:E protein with MEF2
R-HSA-8956568 RUNX1 binds the core TAL1 complex
R-HSA-8956586 RUNX1-containing TAL1 complex binds the MYB gene enhancer
R-HSA-375170 CDO in myogenesis
R-HSA-525793 Myogenesis
R-HSA-1266738 Developmental Biology
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: BHLHB21, E2A, ITF1, NM_001136139, NP_001129611, P15923-2
UCSC ID: uc002ltt.4
RefSeq Accession: NM_001136139
Protein: P15923-2, splice isoform of P15923 CCDS: CCDS45899.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001136139.2
exon count: 19CDS single in 3' UTR: no RNA size: 4078
ORF size: 1956CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3550.00frame shift in genome: no % Coverage: 100.00
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.