ndr1 nodal-related 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: ndr1provided by ZNC
Official Full Name: nodal-related 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-256
See related: Ensembl:ENSDARG00000057096 AllianceGenome:ZFIN:ZDB-GENE-990415-256
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: sqt; NDR2; znr2; Ndr-1; Znr-2; CHUNP6892
Summary: Predicted to enable cytokine activity. Involved in camera-type eye development. Acts upstream of or within several processes, including hypothalamus development; positive regulation of fibroblast growth factor receptor signaling pathway; and regionalization. Part of protein-containing complex. Is expressed in embryonic structure; ovary; posterior lateral line primordium; and unfertilized egg. Human ortholog(s) of this gene implicated in visceral heterotaxy. Orthologous to human NODAL (nodal growth differentiation factor). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 21

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	21	NC_007132.7 (21010919..21013085)
105	previous assembly	GRCz10 (GCF_000002035.5)	21	NC_007132.6 (20974283..20976449)

Chromosome 21 - NC_007132.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

The pattern of nodal morphogen signaling is shaped by co-receptor expression.
Title: The pattern of nodal morphogen signaling is shaped by co-receptor expression.
Nodal signaling triggers an autocrine circuit for initiating endodermal internalization. Activation of the Nodal receptor directs endodermal specification through sox32 and also induces expression of more Nodal ligands. These ligands act in an autocrine fashion to initiate endodermal cell sorting.
Title: Nodal signaling has dual roles in fate specification and directed migration during germ layer segregation in zebrafish.
Collectively, these data indicate that gdf3 is critical for robust Nodal signaling at multiple stages in zebrafish embryonic development.
Title: Gdf3 is required for robust Nodal signaling during germ layer formation and left-right patterning.
Together, these findings demonstrate that Gdf3 is an essential cofactor of Nodal signaling during establishment of the embryonic axis.
Title: Maternal Gdf3 is an obligatory cofactor in Nodal signaling for embryonic axis formation in zebrafish.
Theauthors find that zebrafish lefty mutants exhibit excess Nodal signaling and increased specification of mesendoderm, resulting in embryonic lethality.
Title: Nodal patterning without Lefty inhibitory feedback is functional but fragile.
These results favour a model in which Apelin receptor is required to fine-tune Nodal output, acting as a specific rheostat for the Nodal/TGFbeta pathway during the earliest stages of cardiogenesis.
Title: The Apelin receptor enhances Nodal/TGFβ signaling to ensure proper cardiac development.
Our data do not support the reaction-diffusion model, but instead, we propose that Nodal activates signaling in a temporal window that is defined by a miR-430-mediated delay of Lft1/2 translation
Title: A Temporal Window for Signal Activation Dictates the Dimensions of a Nodal Signaling Domain.
Zebrafish Ldb2a binds and directly activates the I-Smad7 gene, whereas it binds and represses the ligand gene, Squint, which drives positive feedback.
Title: A novel TGFβ modulator that uncouples R-Smad/I-Smad-mediated negative feedback from R-Smad/ligand-driven positive feedback.
support a model wherein sqt RNA acts as a scaffold to bind and deliver/sequester maternal factors to future embryonic dorsal
Title: Dorsal activity of maternal squint is mediated by a non-coding function of the RNA.
results indicate that differential diffusivity is the major determinant of the differences in Nodal/Lefty range and provide biophysical support for reaction-diffusion models of activator/inhibitor-mediated patterning
Title: Differential diffusivity of Nodal and Lefty underlies a reaction-diffusion patterning system.

Submit: New GeneRIF Correction See all GeneRIFs (21)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SQUINT (e-PCR)
- UniSTS:205425

fc04h09.x1 (e-PCR)
- UniSTS:203697

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables cytokine activity	IBA Inferred from Biological aspect of Ancestor more info
enables growth factor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within Spemann organizer formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within anterior/posterior axis specification, embryo	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of dorsal identity	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within determination of left/right asymmetry in lateral mesoderm	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of digestive tract development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of digestive tract development	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within dorsal/ventral axis specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dorsal/ventral pattern formation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within dorsal/ventral pattern formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of endocrine pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of endocrine pancreas development	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within hypothalamus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of liver development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of liver development	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within mesendoderm development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mesoderm development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nodal signaling pathway	TAS Traceable Author Statement more info	PubMed
acts_upstream_of pharyngeal system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of pharyngeal system development	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of developmental process	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within positive regulation of fibroblast growth factor receptor signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of gene expression	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within primitive hemopoiesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within protein processing	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of protein secretion	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
part_of protein-containing complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: nodal-related 1

Names: squint

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_130966.2 → NP_571041.1 nodal-related 1 precursor

See identical proteins and their annotated locations for NP_571041.1

Status: PROVISIONAL

Source sequence(s)

AF056327

UniProtKB/TrEMBL

O13144, Q78CS0

Related

ENSDARP00000074144.3, ENSDART00000079692.4

Conserved Domains (2) summary

pfam00019
Location:291 → 391

TGF_beta; Transforming growth factor beta like domain

pfam00688
Location:56 → 190

TGFb_propeptide; TGF-beta propeptide