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LEF1 lymphoid enhancer binding factor 1 [ Homo sapiens (human) ]

Gene ID: 51176, updated on 12-Jul-2020

Summary

Official Symbol
LEF1provided by HGNC
Official Full Name
lymphoid enhancer binding factor 1provided by HGNC
Primary source
HGNC:HGNC:6551
See related
Ensembl:ENSG00000138795 MIM:153245
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LEF-1; TCF10; TCF7L3; TCF1ALPHA
Summary
This gene encodes a transcription factor belonging to a family of proteins that share homology with the high mobility group protein-1. The protein encoded by this gene can bind to a functionally important site in the T-cell receptor-alpha enhancer, thereby conferring maximal enhancer activity. This transcription factor is involved in the Wnt signaling pathway, and it may function in hair cell differentiation and follicle morphogenesis. Mutations in this gene have been found in somatic sebaceous tumors. This gene has also been linked to other cancers, including androgen-independent prostate cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
Expression
Broad expression in lymph node (RPKM 17.6), appendix (RPKM 8.1) and 14 other tissues See more
Orthologs

Genomic context

See LEF1 in Genome Data Viewer
Location:
4q25
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (108047545..108168956, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (108968701..109090112, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986298 Neighboring gene uncharacterized LOC107986299 Neighboring gene cytochrome P450 family 2 subfamily U member 1 Neighboring gene hydroxyacyl-CoA dehydrogenase Neighboring gene LEF1 antisense RNA 1 Neighboring gene uncharacterized LOC107986300 Neighboring gene VISTA enhancer hs1545

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study identified AFF1 as a susceptibility locus for systemic lupus eyrthematosus in Japanese.
NHGRI GWA Catalog
Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.
NHGRI GWA Catalog
Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction.
NHGRI GWA Catalog
Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat and methamphetamine suppresses expression of LEF-1, a key partner of beta-catenin to regulate cognate gene expression PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ46390, DKFZp586H0919

Gene Ontology Provided by GOA

Function Evidence Code Pubs
C2H2 zinc finger domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA binding, bending ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA-binding transcription activator activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription activator activity, RNA polymerase II-specific IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA polymerase II regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
armadillo repeat domain binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
armadillo repeat domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
beta-catenin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
beta-catenin binding IDA
Inferred from Direct Assay
more info
PubMed 
beta-catenin binding IPI
Inferred from Physical Interaction
more info
PubMed 
beta-catenin binding TAS
Traceable Author Statement
more info
PubMed 
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cysteine-type endopeptidase inhibitor activity involved in apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
estrogen receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
estrogen receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
estrogen receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
gamma-catenin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
gamma-catenin binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone deacetylase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
B cell proliferation IEA
Inferred from Electronic Annotation
more info
 
BMP signaling pathway IEA
Inferred from Electronic Annotation
more info
 
T cell receptor V(D)J recombination IEA
Inferred from Electronic Annotation
more info
 
T-helper 1 cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
Wnt signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Wnt signaling pathway, calcium modulating pathway TAS
Traceable Author Statement
more info
 
anatomical structure regression IEA
Inferred from Electronic Annotation
more info
 
apoptotic process involved in blood vessel morphogenesis IEA
Inferred from Electronic Annotation
more info
 
beta-catenin-TCF complex assembly TAS
Traceable Author Statement
more info
 
branching involved in blood vessel morphogenesis IEA
Inferred from Electronic Annotation
more info
 
canonical Wnt signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
canonical Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
cell chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to cytokine stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to interleukin-4 IDA
Inferred from Direct Assay
more info
PubMed 
chorio-allantoic fusion IEA
Inferred from Electronic Annotation
more info
 
dentate gyrus development IEA
Inferred from Electronic Annotation
more info
 
embryonic limb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
epithelial to mesenchymal transition ISS
Inferred from Sequence or Structural Similarity
more info
 
face morphogenesis IEA
Inferred from Electronic Annotation
more info
 
forebrain neuroblast division IEA
Inferred from Electronic Annotation
more info
 
forebrain radial glial cell differentiation IEA
Inferred from Electronic Annotation
more info
 
formation of radial glial scaffolds IEA
Inferred from Electronic Annotation
more info
 
histone H3 acetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone H4 acetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
mammary gland development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of apoptotic process in bone marrow IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cysteine-type endopeptidase activity involved in apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of estrogen receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of interleukin-13 production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of interleukin-4 production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of interleukin-5 production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of striated muscle tissue development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
neutrophil differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
odontogenesis of dentin-containing tooth IEA
Inferred from Electronic Annotation
more info
 
osteoblast differentiation IEP
Inferred from Expression Pattern
more info
PubMed 
paraxial mesoderm formation IEA
Inferred from Electronic Annotation
more info
 
positive regulation by host of viral transcription IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell proliferation in bone marrow IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of epithelial to mesenchymal transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gamma-delta T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of granulocyte differentiation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of granulocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
regulation of cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
secondary palate development ISS
Inferred from Sequence or Structural Similarity
more info
 
sensory perception of taste IEA
Inferred from Electronic Annotation
more info
 
somitogenesis IEA
Inferred from Electronic Annotation
more info
 
sprouting angiogenesis IEA
Inferred from Electronic Annotation
more info
 
steroid hormone mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
tongue development IEA
Inferred from Electronic Annotation
more info
 
trachea gland development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
beta-catenin-TCF complex IPI
Inferred from Physical Interaction
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IC
Inferred by Curator
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-DNA complex IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
lymphoid enhancer-binding factor 1
Names
T cell-specific transcription factor 1-alpha
TCF1-alpha

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_015798.1 RefSeqGene

    Range
    5025..126409
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001130713.2NP_001124185.1  lymphoid enhancer-binding factor 1 isoform 2

    See identical proteins and their annotated locations for NP_001124185.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
    Source sequence(s)
    AC097067, AC118062, AF288571, AK225772, AL049409
    Consensus CDS
    CCDS47123.1
    UniProtKB/Swiss-Prot
    Q9UJU2
    UniProtKB/TrEMBL
    Q659G9
    Related
    ENSP00000406176.2, ENST00000438313.6
    Conserved Domains (2) summary
    cd01388
    Location:270341
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
    pfam08347
    Location:1213
    CTNNB1_binding; N-terminal CTNNB1 binding
  2. NM_001130714.2NP_001124186.1  lymphoid enhancer-binding factor 1 isoform 3

    See identical proteins and their annotated locations for NP_001124186.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks both an in-frame exon in the central coding region and an exon in the 3' coding region that causes a frameshift, compared to variant 1. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC097067, AF288571, AK225772, AL049409, BC040559
    Consensus CDS
    CCDS47122.1
    UniProtKB/Swiss-Prot
    Q9UJU2
    UniProtKB/TrEMBL
    Q659G9
    Related
    ENSP00000369284.2, ENST00000379951.6
    Conserved Domains (2) summary
    cd01388
    Location:270341
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
    pfam08347
    Location:1213
    CTNNB1_binding; N-terminal CTNNB1 binding
  3. NM_001166119.1NP_001159591.1  lymphoid enhancer-binding factor 1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region, and lacks an alternate in-frame exon in the central coding region, compared to variant 1. The encoded isoform (4) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC118062, AF288571, AK303272, AL049409, DC405840, DC406065
    Consensus CDS
    CCDS54791.1
    UniProtKB/Swiss-Prot
    Q9UJU2
    UniProtKB/TrEMBL
    Q659G9
    Related
    ENSP00000422840.1, ENST00000510624.5
    Conserved Domains (2) summary
    cd01388
    Location:202273
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
    pfam08347
    Location:1145
    CTNNB1_binding; N-terminal CTNNB1 binding
  4. NM_016269.5NP_057353.1  lymphoid enhancer-binding factor 1 isoform 1

    See identical proteins and their annotated locations for NP_057353.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC097067, AF288571, AK225772, AL049409, BC050632
    Consensus CDS
    CCDS3679.1
    UniProtKB/Swiss-Prot
    Q9UJU2
    UniProtKB/TrEMBL
    A0A024RDI7, Q659G9
    Related
    ENSP00000265165.1, ENST00000265165.6
    Conserved Domains (2) summary
    cd01388
    Location:298369
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
    pfam08347
    Location:1213
    CTNNB1_binding; N-terminal CTNNB1 binding

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    108047545..108168956 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005263046.3XP_005263103.1  lymphoid enhancer-binding factor 1 isoform X1

    Conserved Domains (2) summary
    cd01388
    Location:298369
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
    pfam08347
    Location:1213
    CTNNB1_binding; N-terminal CTNNB1 binding
  2. XM_006714233.1XP_006714296.1  lymphoid enhancer-binding factor 1 isoform X4

    Conserved Domains (2) summary
    cd01388
    Location:183254
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
    pfam08347
    Location:198
    CTNNB1_binding; N-terminal CTNNB1 binding
  3. XM_005263048.1XP_005263105.1  lymphoid enhancer-binding factor 1 isoform X3

    Conserved Domains (2) summary
    cd01388
    Location:202273
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
    pfam08347
    Location:1145
    CTNNB1_binding; N-terminal CTNNB1 binding
  4. XM_005263047.1XP_005263104.1  lymphoid enhancer-binding factor 1 isoform X2

    Conserved Domains (2) summary
    cd01388
    Location:230301
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
    pfam08347
    Location:1145
    CTNNB1_binding; N-terminal CTNNB1 binding
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