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

    Gene ID: 30250, updated on 9-Dec-2024

    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, Dec 2024]
    Orthologs
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    Genomic context

    See sema3d in Genome Data Viewer
    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_007129.7Genomic Context describing neighboring genes Neighboring gene transmembrane protein 243, mitochondrial a Neighboring gene endosome-lysosome associated apoptosis and autophagy regulator family member 2a Neighboring gene glutamate receptor, metabotropic 3 Neighboring gene sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Ab Neighboring gene uncharacterized LOC137488253 Neighboring gene sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    General gene information

    Markers

    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

    Preferred Names
    semaphorin-3D
    Names
    sema Z2
    semaphorin 3d
    semaphorin-2
    semaphorin-Z2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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)

    1. NM_131048.2NP_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:599689
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11252
      Location:65538
      Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
      smart00423
      Location:537589
      PSI; domain found in Plexins, Semaphorins and Integrins

    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

    1. NC_007129.7 Reference GRCz11 Primary Assembly

      Range
      9171778..9238675
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)