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

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; AllianceGenome:HGNC:6551
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: mouse all
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Genomic context

Location:: 4q25

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (108047548..108168932, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (111349885..111471256, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (108968704..109090088, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Downregulation of TCF7 and LEF1 is a key determinant of tumor-infiltrating regulatory T-cell function.
Title: Downregulation of TCF7 and LEF1 is a key determinant of tumor-infiltrating regulatory T-cell function.
Altered levels of lymphocyte enhancer-binding factor-1 modulates the pigmentation in acral and non-acral lesions of non-segmental vitiligo patients: a follow-up-based study in North India.
Title: Altered levels of lymphocyte enhancer-binding factor-1 modulates the pigmentation in acral and non-acral lesions of non-segmental vitiligo patients: a follow-up-based study in North India.
A distinct isoform of lymphoid enhancer binding factor 1 (LEF1) epigenetically restricts EBV reactivation to maintain viral latency.
Title: A distinct isoform of lymphoid enhancer binding factor 1 (LEF1) epigenetically restricts EBV reactivation to maintain viral latency.
LEF1 isoforms regulate cellular senescence and aging.
Title: LEF1 isoforms regulate cellular senescence and aging.
Constant small-cell changes and variable LEF1 expression in DUSP22-rearranged primary cutaneous anaplastic large-cell lymphoma: Analysis of the repeated biopsies of three patients.
Title: Constant small-cell changes and variable LEF1 expression in DUSP22-rearranged primary cutaneous anaplastic large-cell lymphoma: Analysis of the repeated biopsies of three patients.
PD1 is transcriptionally regulated by LEF1 in mature T cells.
Title: PD1 is transcriptionally regulated by LEF1 in mature T cells.
Carcinogenesis promotion in oral squamous cell carcinoma: KDM4A complex-mediated gene transcriptional suppression by LEF1.
Title: Carcinogenesis promotion in oral squamous cell carcinoma: KDM4A complex-mediated gene transcriptional suppression by LEF1.
Proteogenomic Profiling of High-Grade B-Cell Lymphoma With 11q Aberrations and Burkitt Lymphoma Reveals Lymphoid Enhancer Binding Factor 1 as a Novel Biomarker.
Title: Proteogenomic Profiling of High-Grade B-Cell Lymphoma With 11q Aberrations and Burkitt Lymphoma Reveals Lymphoid Enhancer Binding Factor 1 as a Novel Biomarker.
PRAME and LEF1 in Combined Deep Penetrating Nevus and Combined Blue Nevus: Utility and Pitfalls.
Title: PRAME and LEF1 in Combined Deep Penetrating Nevus and Combined Blue Nevus: Utility and Pitfalls.
LEF1 Drives a Central Memory Program and Supports Antitumor Activity of Natural Killer T Cells.
Title: LEF1 Drives a Central Memory Program and Supports Antitumor Activity of Natural Killer T Cells.

Submit: New GeneRIF Correction See all GeneRIFs (207)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH122898 (e-PCR)
- UniSTS:135195

SHGC-154060 (e-PCR)
- UniSTS:183869

SHGC-18750 (e-PCR)
- UniSTS:27458

Lef1 (e-PCR), detects polymorphism
- UniSTS:499097

LEF1_1628 (e-PCR)
- UniSTS:277449

SHGC-18753 (e-PCR)
- UniSTS:3285

RH121496 (e-PCR)
- UniSTS:134623

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables C2H2 zinc finger domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables DNA binding, bending	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables armadillo repeat domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables beta-catenin binding	IDA Inferred from Direct Assay more info	PubMed
enables beta-catenin binding	IPI Inferred from Physical Interaction more info	PubMed
enables beta-catenin binding	TAS Traceable Author Statement more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables gamma-catenin binding	IPI Inferred from Physical Interaction more info	PubMed
enables histone deacetylase binding	IPI Inferred from Physical Interaction more info	PubMed
enables nuclear estrogen receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription regulator inhibitor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in B cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in BMP signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in T cell receptor V(D)J recombination	IEA Inferred from Electronic Annotation more info
involved_in T-helper 1 cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in anatomical structure regression	IEA Inferred from Electronic Annotation more info
involved_in apoptotic process involved in blood vessel morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in branching involved in blood vessel morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in canonical Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in cell chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to cytokine stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to interleukin-4	IDA Inferred from Direct Assay more info	PubMed
involved_in chorio-allantoic fusion	IEA Inferred from Electronic Annotation more info
involved_in dentate gyrus development	IEA Inferred from Electronic Annotation more info
involved_in embryonic limb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in epithelial cell apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in epithelial to mesenchymal transition	ISS Inferred from Sequence or Structural Similarity more info
involved_in face morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in forebrain neuroblast division	IEA Inferred from Electronic Annotation more info
involved_in forebrain radial glial cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in formation of radial glial scaffolds	IEA Inferred from Electronic Annotation more info
involved_in mammary gland development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA binding	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of apoptotic process in bone marrow cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of interleukin-13 production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of interleukin-4 production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of interleukin-5 production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of striated muscle tissue development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neutrophil differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in odontogenesis of dentin-containing tooth	IEA Inferred from Electronic Annotation more info
involved_in osteoblast differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in paraxial mesoderm formation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation by host of viral transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell cycle process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell proliferation in bone marrow	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of chondrocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of epithelial to mesenchymal transition	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gamma-delta T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of granulocyte differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of granulocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of odontoblast differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to chromatin	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of neurogenesis	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in secondary palate development	ISS Inferred from Sequence or Structural Similarity more info
involved_in sensory perception of taste	IEA Inferred from Electronic Annotation more info
involved_in somitogenesis	IEA Inferred from Electronic Annotation more info
involved_in sprouting angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in tongue development	IEA Inferred from Electronic Annotation more info
involved_in trachea gland development	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of beta-catenin-TCF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of beta-catenin-TCF complex	IPI Inferred from Physical Interaction more info	PubMed
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IC Inferred by Curator more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of protein-DNA complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: lymphoid enhancer-binding factor 1

Names: T cell-specific transcription factor 1-alpha; TCF1-alpha

NCBI Reference Sequences (RefSeq)

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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

NG_015798.1 RefSeqGene

Range

5025..126409

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001130713.3 → NP_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:270 → 341

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:1 → 213

CTNNB1_binding; N-terminal CTNNB1 binding
NM_001130714.3 → NP_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:270 → 341

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:1 → 213

CTNNB1_binding; N-terminal CTNNB1 binding
NM_001166119.2 → NP_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

Consensus CDS

CCDS54791.1

UniProtKB/TrEMBL

B4DZY5

Related

ENSP00000422840.1, ENST00000510624.5

Conserved Domains (2) summary

cd01388
Location:202 → 273

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:1 → 145

CTNNB1_binding; N-terminal CTNNB1 binding
NM_016269.5 → NP_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

B4DG38, B7Z8E2, E9PDK3, Q3ZCU4, Q9HAZ0, Q9UJU2

Related

ENSP00000265165.1, ENST00000265165.6

Conserved Domains (2) summary

cd01388
Location:298 → 369

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:1 → 213

CTNNB1_binding; N-terminal CTNNB1 binding

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

108047548..108168932 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005263046.4 → XP_005263103.1 lymphoid enhancer-binding factor 1 isoform X1

Conserved Domains (2) summary

cd01388
Location:298 → 369

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:1 → 213

CTNNB1_binding; N-terminal CTNNB1 binding
XM_006714233.2 → XP_006714296.1 lymphoid enhancer-binding factor 1 isoform X4

UniProtKB/TrEMBL

B4DZY5

Conserved Domains (2) summary

cd01388
Location:183 → 254

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:1 → 98

CTNNB1_binding; N-terminal CTNNB1 binding
XM_005263048.1 → XP_005263105.1 lymphoid enhancer-binding factor 1 isoform X3

Conserved Domains (2) summary

cd01388
Location:202 → 273

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:1 → 145

CTNNB1_binding; N-terminal CTNNB1 binding
XM_005263047.1 → XP_005263104.1 lymphoid enhancer-binding factor 1 isoform X2

Conserved Domains (2) summary

cd01388
Location:230 → 301

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:1 → 145

CTNNB1_binding; N-terminal CTNNB1 binding

RNA

XR_007057926.1 RNA Sequence
XR_007057925.1 RNA Sequence
XR_007057927.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060928.1 Alternate T2T-CHM13v2.0

Range

111349885..111471256 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054350153.1 → XP_054206128.1 lymphoid enhancer-binding factor 1 isoform X1
XM_054350156.1 → XP_054206131.1 lymphoid enhancer-binding factor 1 isoform X4

UniProtKB/TrEMBL

B4DZY5
XM_054350155.1 → XP_054206130.1 lymphoid enhancer-binding factor 1 isoform X3
XM_054350154.1 → XP_054206129.1 lymphoid enhancer-binding factor 1 isoform X2