gdf3 growth differentiation factor 3 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: gdf3provided by ZNC
Official Full Name: growth differentiation factor 3provided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-389
See related: Ensembl:ENSDARG00000037995 AllianceGenome:ZFIN:ZDB-GENE-980526-389
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: VG1; dvr1; DVR-1; cb556; zDVR1; zDVR-1; zgc:103542
Summary: Predicted to enable cytokine activity. Involved in regulation of epiboly involved in gastrulation with mouth forming second. Acts upstream of or within with a positive effect on nodal signaling pathway. Acts upstream of or within with a negative effect on BMP signaling pathway. Acts upstream of or within several processes, including axis specification; embryonic morphogenesis; and regulation of nodal signaling pathway. Part of protein-containing complex. Is expressed in several structures, including blastomere; gonad; heart primordium; mesoderm; and tail bud. Human ortholog(s) of this gene implicated in Klippel-Feil syndrome 3; congenital heart disease; isolated microphthalmia 7; multiple types of congenital heart defects 6; and visceral heterotaxy. Orthologous to several human genes including GDF3 (growth differentiation factor 3). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 17

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	17	NC_007128.7 (4239433..4252228, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	17	NC_007128.6 (4080983..4087098, complement)

Chromosome 17 - NC_007128.7 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
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?

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.
Dvr1 acts as a direct and essential mediator for convergence and extension cell movements during zebrafish gastrulation.
Title: Setdb2 controls convergence and extension movements during zebrafish gastrulation by transcriptional regulation of dvr1.
Dvr1 is responsible for enabling the transfer of a left-right signal from Kupffer's vesicle to lateral plate mesoderm.
Title: Dvr1 transfers left-right asymmetric signals from Kupffer's vesicle to lateral plate mesoderm in zebrafish.
serum Vg in zebrafish D. rerio is an acute phase protein with bacterial-binding and inhibiting activities.
Title: Vitellogenin is an acute phase protein with bacterial-binding and inhibiting activities.
Vg1 signaling in zebrafish depends on EGF-CFC proteins, but not on Nodal signals. Vg1 binds to and signal through Activin receptors only in the presence of EGF-CFC proteins.
Title: EGF-CFC proteins are essential coreceptors for the TGF-beta signals Vg1 and GDF1.

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General gene information

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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

Process	Evidence Code	Pubs
acts_upstream_of_or_within_negative_effect BMP signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within axis specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within convergent extension involved in gastrulation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within convergent extension involved in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within left/right pattern formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nodal signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within_positive_effect nodal signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of cell division	IEA Inferred from Electronic Annotation more info
involved_in regulation of epiboly involved in gastrulation with mouth forming second	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of nodal signaling pathway	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: protein DVR-1

Names: decapentaplegic and Vg-related 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_130948.1 → NP_571023.1 protein DVR-1 precursor

See identical proteins and their annotated locations for NP_571023.1

Status: PROVISIONAL

Source sequence(s)

U00931

UniProtKB/Swiss-Prot

P35621

Related

ENSDARP00000055378.4, ENSDART00000055379.6

Conserved Domains (2) summary

smart00204
Location:254 → 355

TGFB; Transforming growth factor-beta (TGF-beta) family

pfam00688
Location:27 → 200

TGFb_propeptide; TGF-beta propeptide

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_007128.7 Reference GRCz11 Primary Assembly

Range

4239433..4252228 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_068214320.1 → XP_068070421.1 protein DVR-1 isoform X1
XM_021467105.2 → XP_021322780.1 protein DVR-1 isoform X1

UniProtKB/TrEMBL

A0A8M9PNK2

Related

ENSDARP00000126546.1, ENSDART00000151851.3

Conserved Domains (2) summary

smart00204
Location:221 → 322

TGFB; Transforming growth factor-beta (TGF-beta) family

pfam00688
Location:1 → 167

TGFb_propeptide; TGF-beta propeptide
XM_068214318.1 → XP_068070419.1 protein DVR-1 isoform X1
XM_068214317.1 → XP_068070418.1 protein DVR-1 isoform X1
XM_068214319.1 → XP_068070420.1 protein DVR-1 isoform X1