lef1 lymphoid enhancer-binding factor 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: lef1provided by ZNC
Official Full Name: lymphoid enhancer-binding factor 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-990714-26
See related: Ensembl:ENSDARG00000031894 AllianceGenome:ZFIN:ZDB-GENE-990714-26
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Summary: Enables sequence-specific DNA binding activity. Involved in regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including fin development; fin regeneration; and forebrain development. Predicted to be located in chromatin. Predicted to be part of beta-catenin-TCF complex. Is expressed in several structures, including midbrain hindbrain boundary neural rod; nervous system; neural crest; pleuroperitoneal region; and trunk. Used to study anxiety disorder. Human ortholog(s) of this gene implicated in ovarian cancer. Orthologous to human LEF1 (lymphoid enhancer binding factor 1). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 1

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	1	NC_007112.7 (49814524..49903487)
105	previous assembly	GRCz10 (GCF_000002035.5)	1	NC_007112.6 (49170722..49259661)

Chromosome 1 - NC_007112.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Data suggest that LEF1-dependent genes in zebrafish hypothalamus are associated with anxiety; LEF1 null mutant zebrafish exhibit increased anxiety.
Title: Lef1-dependent hypothalamic neurogenesis inhibits anxiety.
mesodermal Wnt3a-mediated signaling via the transcription factor Lef1 positively regulates EC specification (defined by kdrl expression) at the expense of primitive erythrocyte specification (defined by gata1 expression) in zebrafish embryos.
Title: Wnt signaling positively regulates endothelial cell fate specification in the Fli1a-positive progenitor population via Lef1.
Amotl2a function in the control of lateral line primordium cell proliferation is mediated together by the Hippo pathway effector Yap1 and the Wnt/beta-catenin effector Lef1.
Title: Amotl2a interacts with the Hippo effector Yap1 and the Wnt/β-catenin effector Lef1 to control tissue size in zebrafish.
Lef1 has a role in regulating Dusp6 in formation of the zebrafish posterior lateral line primordium
Title: Lef1 regulates Dusp6 to influence neuromast formation and spacing in the zebrafish posterior lateral line primordium.
Nlk2 is essential for the phosphorylation and activation of Lef1 transcriptional activity in neural progenitor cells.
Title: NLK positively regulates Wnt/β-catenin signalling by phosphorylating LEF1 in neural progenitor cells.
Lef1 sustains proliferation of leading zone progenitors, maintaining the primordium size and defining neuromast deposition rate.
Title: Lef1-dependent Wnt/β-catenin signalling drives the proliferative engine that maintains tissue homeostasis during lateral line development.
Lef1 is required for progenitor cell identity in the zebrafish lateral line primordium.
Title: Lef1 is required for progenitor cell identity in the zebrafish lateral line primordium.
Data conclude that lef1-mediated Wnt signaling is involved in various aspects of primordium migration, although part of this implication is masked by a high level of developmental redundancy.
Title: Lef1 controls patterning and proliferation in the posterior lateral line system of zebrafish.
Data show cooperation between Dnmt3 and an H3K9 methyltransferase G9a in regulating lef1.
Title: Dnmt3 and G9a cooperate for tissue-specific development in zebrafish.
Domain-specific regulation of foxP2 CNS expression by lef1.
Title: Domain-specific regulation of foxP2 CNS expression by lef1.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

lef1 (e-PCR), detects polymorphism
- UniSTS:205579

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
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 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	TAS Traceable Author Statement more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific DNA binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within canonical Wnt signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within canonical Wnt signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within caudal fin development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within forebrain neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hypothalamus cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hypothalamus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within muscle cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural crest cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neurogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pectoral fin development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within posterior lateral line development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within posterior lateral line neuromast deposition	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within posterior lateral line neuromast development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of cell proliferation involved in tissue homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of retinoic acid biosynthetic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within somitogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of beta-catenin-TCF complex	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: lymphoid enhancer-binding factor 1

Names: etID310027.1; lymphocyte enhancer binding factor 1

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.

mRNA and Protein(s)

NM_131426.2 → NP_571501.1 lymphoid enhancer-binding factor 1

See identical proteins and their annotated locations for NP_571501.1

Status: VALIDATED

Source sequence(s)

BX572104, CR391978

UniProtKB/TrEMBL

B3DFM5, Q9W7C0

Related

ENSDARP00000114249.2, ENSDART00000132405.4

Conserved Domains (2) summary

cd01388
Location:264 → 335

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 → 210

CTNNB1_binding; N-terminal CTNNB1 binding

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007112.7 Reference GRCz11 Primary Assembly

Range

49814524..49903487

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_068222904.1 → XP_068079005.1 lymphoid enhancer-binding factor 1 isoform X3
XM_068222873.1 → XP_068078974.1 lymphoid enhancer-binding factor 1 isoform X1
XM_068222916.1 → XP_068079017.1 lymphoid enhancer-binding factor 1 isoform X4
XM_068222929.1 → XP_068079030.1 lymphoid enhancer-binding factor 1 isoform X5

Related

ENSDARP00000132999.2, ENSDART00000164936.2
XM_068222889.1 → XP_068078990.1 lymphoid enhancer-binding factor 1 isoform X2