sema3d sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sema3dprovided by ZNC
Official Full Name: sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Dprovided by ZNC
Primary source: ZFIN:ZDB-GENE-990715-2
See related: Ensembl:ENSDARG00000017369 AllianceGenome:ZFIN:ZDB-GENE-990715-2
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
Also known as: sema2; semaZ2
Summary: Enables neuropilin binding activity. Acts upstream of or within several processes, including axon development; heart development; and skeletal system development. Predicted to be located in extracellular region. Predicted to be active in extracellular space and plasma membrane. Is expressed in several structures, including central nervous system; hindbrain neural keel; neural crest; notochord; and posterior lateral line system. Orthologous to human SEMA3D (semaphorin 3D). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 18

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	18	NC_007129.7 (9171778..9238675)
105	previous assembly	GRCz10 (GCF_000002035.5)	18	NC_007129.6 (9213759..9280656)

Chromosome 18 - NC_007129.7 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?

Sema3d regulates collective endothelial cell migration in zebrafish through two separate mechanisms. Mesenchymal Sema3d guides outgrowth of the common cardinal vein via repulsion and signals through PlexinD1.
Title: Sema3d controls collective endothelial cell migration by distinct mechanisms via Nrp1 and PlxnD1.
Hapln1a-ECM stabilizes the secreted growth factor Semaphorin3d (Sema3d), which has been independently shown to mediate Cx43 dependent phenotypes during regeneration.
Title: Cx43-Dependent Skeletal Phenotypes Are Mediated by Interactions between the Hapln1a-ECM and Sema3d during Fin Regeneration.
Sema3d functions in a common molecular pathway with Cx43 in cell proliferation and joint formation
Title: Semaphorin3d mediates Cx43-dependent phenotypes during fin regeneration.
We show that Semaphorin3D (Sema3D), a classic repulsive molecule, promotes fasciculation by regulating L1 CAM levels and axon-axon interactions rather than by creating a repulsive surround.
Title: Semaphorin3D regulates axon axon interactions by modulating levels of L1 cell adhesion molecule.
Sema3d knockdown reduces markers of migratory neural crest cell (NCC) and disrupts NCC-derived tissues.
Title: Semaphorin 3d promotes cell proliferation and neural crest cell development downstream of TCF in the zebrafish hindbrain.
Data show that Hedgehog signaling is required for commissure formation, glial bridge formation, and the restricted expression of the guidance molecules slit1a, slit2, slit3 and sema3d.
Title: Hedgehog regulated Slit expression determines commissure and glial cell position in the zebrafish forebrain.
proper balance of Sema3d is needed at the midline for the progression of retinal ganglion cell axons from the chiasm midline into the contralateral optic tract
Title: Semaphorin 3d guides laterality of retinal ganglion cell projections in zebrafish.
Sema3D acts in concert with Nrp1a to guide neurons on the left side of the brain to innervate the target nucleus differently than those on the right side.
Title: Neuropilin asymmetry mediates a left-right difference in habenular connectivity.
We investigated the role of Semaphorin3D (Sema3D) in the formation of the early axon pathways in the zebrafish CNS.
Title: Repulsion and attraction of axons by semaphorin3D are mediated by different neuropilins in vivo.
We propose that a population of sema3D-dependent neural crest cells follow a novel migratory pathway, perhaps toward nrp1A-expressing LPM, and serve as an important early source of cardiomyocytes in the primary heart field.
Title: Semaphorin3D regulates invasion of cardiac neural crest cells into the primary heart field.

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General gene information

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Markers

fb95a06.x1 (e-PCR)
- UniSTS:191859

sema2 (e-PCR)
- UniSTS:205508

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info
enables neuropilin binding	IBA Inferred from Biological aspect of Ancestor more info
enables neuropilin binding	IDA Inferred from Direct Assay more info	PubMed
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in axon guidance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within axonal fasciculation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within blood vessel endothelial cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cardioblast differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell proliferation in hindbrain	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic heart tube development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic skeletal joint morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within enteric nervous system development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within enteric nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin regeneration	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within fin regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within larval heart development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neural crest cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural crest cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neural crest cell migration	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neural crest cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within olfactory bulb axon guidance	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within olfactory bulb axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within peripheral nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within peripheral nervous system neuron axonogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within peripheral nervous system neuron axonogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of axon extension	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retinal ganglion cell axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within thymus development	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
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: semaphorin-3D

Names: sema Z2; semaphorin 3d; semaphorin-2; semaphorin-Z2

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_131048.2 → NP_571123.2 semaphorin-3D precursor

Status: VALIDATED

Source sequence(s)

CU633862, CU855784, CU861648

UniProtKB/Swiss-Prot

Q9W6G6

UniProtKB/TrEMBL

A0A8N7UZF9, E9QD84

Related

ENSDARP00000091966.5, ENSDART00000101192.7

Conserved Domains (3) summary

cd05871
Location:599 → 689

Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin

cd11252
Location:65 → 538

Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)

smart00423
Location:537 → 589

PSI; domain found in Plexins, Semaphorins and Integrins