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    si:dkey-49n23.1 si:dkey-49n23.1 [ Danio rerio (zebrafish) ]

    Gene ID: 558742, updated on 11-Apr-2024

    Summary

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    Official Symbol
    si:dkey-49n23.1provided by ZNC
    Official Full Name
    si:dkey-49n23.1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-050208-762
    See related
    Ensembl:ENSDARG00000040920 AllianceGenome:ZFIN:ZDB-GENE-050208-762
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Summary
    Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Predicted to be involved in several processes, including generation of neurons; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    all
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    Genomic context

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    See si:dkey-49n23.1 in Genome Data Viewer
    Location:
    chromosome: 22
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 22 NC_007133.7 (30812246..30935514, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 22 NC_007133.6 (30863000..30986301, complement)

    Chromosome 22 - NC_007133.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101882696 Neighboring gene uncharacterized LOC797542 Neighboring gene ssu-2 homolog, tandem duplicate 1 Neighboring gene ssu-2 homolog, tandem duplicate 2

    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. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    		  
    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
    		  
    Component Evidence Code Pubs
    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

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007133.7 Reference GRCz11 Primary Assembly

      Range
      30812246..30935514 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_682000.8 → XP_687092.1  semaphorin-3D

      UniProtKB/TrEMBL
      A0A8N7UVR2, F1Q5G8, F1R064
      Related
      ENSDARP00000113231.2, ENSDART00000133335.3
      Conserved Domains (3) summary
      cd05871
      Location:581 → 672
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11239
      Location:48 → 521
      Sema_3; The Sema domain, a protein interacting module, of class 3 semaphorins
      smart00423
      Location:520 → 557
      PSI; domain found in Plexins, Semaphorins and Integrins

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018395121.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      116199..236426 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021473549.1 → XP_021329224.1  semaphorin-3D

      UniProtKB/TrEMBL
      A0A8M9PQE2
      Conserved Domains (3) summary
      cd05871
      Location:581 → 672
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11239
      Location:48 → 521
      Sema_3; The Sema domain, a protein interacting module, of class 3 semaphorins
      smart00423
      Location:520 → 557
      PSI; domain found in Plexins, Semaphorins and Integrins

    2. XM_021473548.1 → XP_021329223.1  semaphorin-3D

      UniProtKB/TrEMBL
      A0A8M9PQE2
      Conserved Domains (3) summary
      cd05871
      Location:581 → 672
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11239
      Location:48 → 521
      Sema_3; The Sema domain, a protein interacting module, of class 3 semaphorins
      smart00423
      Location:520 → 557
      PSI; domain found in Plexins, Semaphorins and Integrins
    Nucleotide Protein Strain
    Heading Accession and Version

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