Human Gene LEF1 (ENST00000265165.6_9) from GENCODE V47lift37
  Description: lymphoid enhancer binding factor 1, transcript variant 1 (from RefSeq NM_016269.5)
Gencode Transcript: ENST00000265165.6_9
Gencode Gene: ENSG00000138795.10_14
Transcript (Including UTRs)
   Position: hg19 chr4:108,968,704-109,090,088 Size: 121,385 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr4:108,984,785-109,088,923 Size: 104,139 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:108,968,704-109,090,088)mRNA (may differ from genome)Protein (399 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LEF1_HUMAN
DESCRIPTION: RecName: Full=Lymphoid enhancer-binding factor 1; Short=LEF-1; AltName: Full=T cell-specific transcription factor 1-alpha; Short=TCF1-alpha;
FUNCTION: Participates in the Wnt signaling pathway. Activates transcription of target genes in the presence of CTNNB1 and EP300. May play a role in hair cell differentiation and follicle morphogenesis. TLE1, TLE2, TLE3 and TLE4 repress transactivation mediated by LEF1 and CTNNB1. Regulates T-cell receptor alpha enhancer function. Binds DNA in a sequence-specific manner. PIAG antagonizes both Wnt-dependent and Wnt-independent activation by LEF1 (By similarity). Isoform 3 lacks the CTNNB1 interaction domain and may be an antagonist for Wnt signaling. Isoform 5 transcriptionally activates the fibronectin promoter, binds to and represses transcription from the E-cadherin promoter in a CTNNB1- independent manner, and is involved in reducing cellular aggregation and increasing cell migration of pancreatic cancer cells. Isoform 1 transcriptionally activates MYC and CCND1 expression and enhances proliferation of pancreatic tumor cells.
SUBUNIT: Binds the armadillo repeat of CTNNB1 and forms a stable complex. Interacts with EP300, TLE1 and PIASG (By similarity). Binds ALYREF/THOC4, MDFI and MDFIC. Interacts with NLK.
SUBCELLULAR LOCATION: Nucleus (By similarity). Note=Found in nuclear bodies upon PIASG binding (By similarity).
TISSUE SPECIFICITY: Detected in thymus. Not detected in normal colon, but highly expressed in colon cancer biopsies and colon cancer cell lines. Expressed in several pancreatic tumors and weakly expressed in normal pancreatic tissue. Isoforms 1 and 5 are detected in several pancreatic cell lines.
DOMAIN: Proline-rich and acidic regions are implicated in the activation functions of RNA polymerase II transcription factors.
PTM: Phosphorylated at Thr-155 and/or Ser-166 by NLK. Phosphorylation by NLK at these sites represses LEF1-mediated transcriptional activation of target genes of the canonical Wnt signaling pathway.
SIMILARITY: Belongs to the TCF/LEF family.
SIMILARITY: Contains 1 HMG box DNA-binding domain.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: LEF1
Diseases sorted by gene-association score: colorectal cancer (7), severe congenital neutropenia (6), prostate cancer (3), arrhythmogenic right ventricular cardiomyopathy (2), skin pilomatrix carcinoma (2), hepatocellular carcinoma (2), chronic lymphocytic leukemia (2), yellow nail syndrome (1), pulmonary immaturity (1)

-  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: 9.62 RPKM in Testis
Total median expression: 90.11 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 -554.501165-0.476 Picture PostScript Text
3' UTR -273.401210-0.226 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
IPR013558 - CTNNB1-bd_N
IPR009071 - HMG_superfamily
IPR024940 - TCF/LEF

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 Q9UJU2
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding
GO:0005515 protein binding
GO:0008013 beta-catenin binding
GO:0008134 transcription factor binding
GO:0008301 DNA binding, bending
GO:0030284 estrogen receptor activity
GO:0030331 estrogen receptor binding
GO:0035326 enhancer binding
GO:0042393 histone binding
GO:0042826 histone deacetylase binding
GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding
GO:0045295 gamma-catenin binding
GO:0070016 armadillo repeat domain binding
GO:0070742 C2H2 zinc finger domain binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001569 branching involved in blood vessel morphogenesis
GO:0001649 osteoblast differentiation
GO:0001755 neural crest cell migration
GO:0001756 somitogenesis
GO:0001837 epithelial to mesenchymal transition
GO:0001944 vasculature development
GO:0002040 sprouting angiogenesis
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0007223 Wnt signaling pathway, calcium modulating pathway
GO:0008284 positive regulation of cell proliferation
GO:0010628 positive regulation of gene expression
GO:0010718 positive regulation of epithelial to mesenchymal transition
GO:0016055 Wnt signaling pathway
GO:0016202 regulation of striated muscle tissue development
GO:0021542 dentate gyrus development
GO:0021766 hippocampus development
GO:0021854 hypothalamus development
GO:0021861 forebrain radial glial cell differentiation
GO:0021873 forebrain neuroblast division
GO:0021879 forebrain neuron differentiation
GO:0021943 formation of radial glial scaffolds
GO:0022407 regulation of cell-cell adhesion
GO:0022408 negative regulation of cell-cell adhesion
GO:0022409 positive regulation of cell-cell adhesion
GO:0030111 regulation of Wnt signaling pathway
GO:0030223 neutrophil differentiation
GO:0030307 positive regulation of cell growth
GO:0030326 embryonic limb morphogenesis
GO:0030335 positive regulation of cell migration
GO:0030509 BMP signaling pathway
GO:0030854 positive regulation of granulocyte differentiation
GO:0030879 mammary gland development
GO:0032696 negative regulation of interleukin-13 production
GO:0032713 negative regulation of interleukin-4 production
GO:0032714 negative regulation of interleukin-5 production
GO:0033153 T cell receptor V(D)J recombination
GO:0042100 B cell proliferation
GO:0042475 odontogenesis of dentin-containing tooth
GO:0043066 negative regulation of apoptotic process
GO:0043154 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0043392 negative regulation of DNA binding
GO:0043401 steroid hormone mediated signaling pathway
GO:0043586 tongue development
GO:0043923 positive regulation by host of viral transcription
GO:0043966 histone H3 acetylation
GO:0043967 histone H4 acetylation
GO:0045063 T-helper 1 cell differentiation
GO:0045843 negative regulation of striated muscle tissue development
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046632 alpha-beta T cell differentiation
GO:0048069 eye pigmentation
GO:0048341 paraxial mesoderm formation
GO:0048468 cell development
GO:0048747 muscle fiber development
GO:0050909 sensory perception of taste
GO:0060033 anatomical structure regression
GO:0060070 canonical Wnt signaling pathway
GO:0060325 face morphogenesis
GO:0060326 cell chemotaxis
GO:0060561 apoptotic process involved in morphogenesis
GO:0060710 chorio-allantoic fusion
GO:0061153 trachea gland development
GO:0071345 cellular response to cytokine stimulus
GO:0071353 cellular response to interleukin-4
GO:0071864 positive regulation of cell proliferation in bone marrow
GO:0071866 negative regulation of apoptotic process in bone marrow
GO:0071895 odontoblast differentiation
GO:0071899 negative regulation of estrogen receptor binding
GO:0090068 positive regulation of cell cycle process
GO:0090090 negative regulation of canonical Wnt signaling pathway
GO:1902262 apoptotic process involved in blood vessel morphogenesis
GO:1904837 beta-catenin-TCF complex assembly

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0005737 cytoplasm
GO:0032993 protein-DNA complex
GO:1990907 beta-catenin-TCF complex


-  Descriptions from all associated GenBank mRNAs
  AF288571 - Homo sapiens lymphoid enhancer factor-1 (LEF1) mRNA, complete cds.
LP896337 - Sequence 1201 from Patent EP3253886.
BC040559 - Homo sapiens lymphoid enhancer-binding factor 1, mRNA (cDNA clone MGC:41818 IMAGE:5269696), complete cds.
BC050632 - Homo sapiens lymphoid enhancer-binding factor 1, mRNA (cDNA clone MGC:60112 IMAGE:6054813), complete cds.
AK303143 - Homo sapiens cDNA FLJ54043 complete cds, highly similar to Lymphoid enhancer-binding factor 1.
AK294395 - Homo sapiens cDNA FLJ61109 complete cds, highly similar to Lymphoid enhancer-binding factor 1.
AK303272 - Homo sapiens cDNA FLJ58716 complete cds, highly similar to Lymphoid enhancer-binding factor 1.
AK225772 - Homo sapiens mRNA for lymphoid enhancer binding factor-1 variant, clone: FCC133A10.
AF198532 - Homo sapiens lymphoid enhancer binding factor-1 mRNA, complete cds.
AF294627 - Homo sapiens lymphoid enhancer factor 1 isoform (LEF1) mRNA, complete cds.
KJ893843 - Synthetic construct Homo sapiens clone ccsbBroadEn_03237 LEF1 gene, encodes complete protein.
EU446873 - Synthetic construct Homo sapiens clone IMAGE:100070042; IMAGE:100012082; FLH257387.01L lymphoid enhancer-binding factor 1 (LEF1) gene, encodes complete protein.
AB463848 - Synthetic construct DNA, clone: pF1KB7666, Homo sapiens LEF1 gene for lymphoid enhancer-binding factor 1, without stop codon, in Flexi system.
CU690754 - Synthetic construct Homo sapiens gateway clone IMAGE:100021390 5' read LEF1 mRNA.
AK128255 - Homo sapiens cDNA FLJ46390 fis, clone THYMU3001593.
AL049409 - Homo sapiens mRNA; cDNA DKFZp586H0919 (from clone DKFZp586H0919).
JD061034 - Sequence 42058 from Patent EP1572962.
JD172469 - Sequence 153493 from Patent EP1572962.
JD538503 - Sequence 519527 from Patent EP1572962.
JD354502 - Sequence 335526 from Patent EP1572962.
JD449475 - Sequence 430499 from Patent EP1572962.
JD312336 - Sequence 293360 from Patent EP1572962.
JD048544 - Sequence 29568 from Patent EP1572962.
JD095723 - Sequence 76747 from Patent EP1572962.
JD554569 - Sequence 535593 from Patent EP1572962.
JD196428 - Sequence 177452 from Patent EP1572962.
JD124620 - Sequence 105644 from Patent EP1572962.
JD110683 - Sequence 91707 from Patent EP1572962.
JD037877 - Sequence 18901 from Patent EP1572962.
JD437240 - Sequence 418264 from Patent EP1572962.
JD176121 - Sequence 157145 from Patent EP1572962.
AF086339 - Homo sapiens full length insert cDNA clone ZD59F01.
JD389972 - Sequence 370996 from Patent EP1572962.
JD461612 - Sequence 442636 from Patent EP1572962.
JD358212 - Sequence 339236 from Patent EP1572962.
JD460543 - Sequence 441567 from Patent EP1572962.
JD406151 - Sequence 387175 from Patent EP1572962.
JD398547 - Sequence 379571 from Patent EP1572962.
JD260876 - Sequence 241900 from Patent EP1572962.
JD173776 - Sequence 154800 from Patent EP1572962.

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

Protein Q9UJU2 (Reactome details) participates in the following event(s):

R-HSA-8944352 TCF/LEF binds WNT promoters
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-4411367 TCF7L1/TCF7L2/LEF1:CTNNB1 bind the MYC gene
R-HSA-8951428 RUNX3 binds CTNNB1:TCF7L2,(LEF1,TCF7L1,TCF7)
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-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-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-162582 Signal Transduction
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: B4DG38, B7Z8E2, E9PDK3, ENST00000265165.1, ENST00000265165.2, ENST00000265165.3, ENST00000265165.4, ENST00000265165.5, LEF1 , LEF1_HUMAN, NM_016269, Q3ZCU4, Q9HAZ0, Q9UJU2, uc317hzf.1, uc317hzf.2
UCSC ID: ENST00000265165.6_9
RefSeq Accession: NM_016269.5
Protein: Q9UJU2 (aka LEF1_HUMAN)

-  Gene Model Information
  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.