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    sema3e sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E [ Danio rerio (zebrafish) ]

    Gene ID: 565658, updated on 15-Dec-2024

    Summary

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    Official Symbol
    sema3eprovided by ZNC
    Official Full Name
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Eprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-7864
    See related
    Ensembl:ENSDARG00000036571 AllianceGenome:ZFIN:ZDB-GENE-030131-7864
    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
    fj37c11; wu:fj37c11; si:ch211-120m13.2
    Summary
    Enables neuropilin binding activity. Acts upstream of or within neural crest cell migration and sprouting angiogenesis. Predicted to be active in extracellular space and plasma membrane. Is expressed in several structures, including cardiovascular system; endoderm; head; immature eye; and nervous system. Used to study CHARGE syndrome. Orthologous to human SEMA3E (semaphorin 3E). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See sema3e in Genome Data Viewer
    Location:
    chromosome: 18
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 18 NC_007129.7 (9448375..9578843)
    105 previous assembly GRCz10 (GCF_000002035.5) 18 NC_007129.6 (9485833..9607821)

    Chromosome 18 - NC_007129.7Genomic Context describing neighboring genes Neighboring gene sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D Neighboring gene sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Ab Neighboring gene uncharacterized LOC137488253 Neighboring gene piccolo presynaptic cytomatrix protein b Neighboring gene voltage-dependent calcium channel subunit alpha-2/delta-1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Plexin B3 guides axons to cross the midline in vivo. Liu ZZ, et al. Front Cell Neurosci, 2024. PMID 38628398, Free PMC Article
    2. Antagonistic interactions among Plexins regulate the timing of intersegmental vessel formation. Lamont RE, et al. Dev Biol, 2009 Jul 15. PMID 19422817
    3. cAMP-induced expression of neuropilin1 promotes retinal axon crossing in the zebrafish optic chiasm. Dell AL, et al. J Neurosci, 2013 Jul 3. PMID 23825413, Free PMC Article
    4. Expression of multiple class three semaphorins in the retina and along the path of zebrafish retinal axons. Callander DC, et al. Dev Dyn, 2007 Oct. PMID 17879313
    5. Sema3E is required for migration of cranial neural crest cells in zebrafish: Implications for the pathogenesis of CHARGE syndrome. Liu ZZ, et al. Int J Exp Pathol, 2019 Aug. PMID 31464029, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Semaphorin sema3E is involved in the pathogenesis of CHARGE syndrome by modulating cranial neural crest cell migration
      Title: Sema3E is required for migration of cranial neural crest cells in zebrafish: Implications for the pathogenesis of CHARGE syndrome.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within sprouting angiogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    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-3E
    Names
    semaphorin 3E

    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)

    1. NM_001045084.1 → NP_001038549.1  semaphorin-3E precursor

      Status: PROVISIONAL

      Source sequence(s)
      BX000697
      UniProtKB/TrEMBL
      A0A8M1N9X0, Q1LYS1
      Related
      ENSDARP00000053124.6, ENSDART00000053125.7
      Conserved Domains (3) summary
      cd05871
      Location:580 → 668
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11253
      Location:46 → 516
      Sema_3E; The Sema domain, a protein interacting module, of semaphorin 3E (Sema3E)
      smart00423
      Location:515 → 563
      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
      9448375..9578843
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068214807.1 → XP_068070908.1  semaphorin-3E isoform X2

    2. XM_021467675.2 → XP_021323350.1  semaphorin-3E isoform X1

      UniProtKB/TrEMBL
      A0A8M9PQA6
      Conserved Domains (3) summary
      cd05871
      Location:579 → 667
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11253
      Location:46 → 516
      Sema_3E; The Sema domain, a protein interacting module, of semaphorin 3E (Sema3E)
      smart00423
      Location:515 → 563
      PSI; domain found in Plexins, Semaphorins and Integrins

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018395006.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      239857..323646
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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