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    sema6ca sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6Ca [ Danio rerio (zebrafish) ]

    Gene ID: 406272, updated on 2-Nov-2024

    Summary

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    Official Symbol
    sema6caprovided by ZNC
    Official Full Name
    sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6Caprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-1933
    See related
    Ensembl:ENSDARG00000002748 AllianceGenome:ZFIN:ZDB-GENE-040426-1933
    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
    sema6d; zgc:56170; wu:fi06a12; wu:fi76a10
    Summary
    Predicted to enable chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Acts upstream of or within axonogenesis; branching involved in blood vessel morphogenesis; and optic cup morphogenesis involved in camera-type eye development. Predicted to be located in membrane. Predicted to be active in plasma membrane. Is expressed in blood vessel; central nervous system; neural rod; optic vesicle; and retina. Orthologous to several human genes including SEMA6C (semaphorin 6C). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    all
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    Genomic context

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    See sema6ca in Genome Data Viewer
    Location:
    chromosome: 19
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (390297..417381)
    105 previous assembly GRCz10 (GCF_000002035.5) 19 NC_007130.6 (390090..417174)

    Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene vacuolar protein sorting 72 homolog a Neighboring gene tumor necrosis factor, alpha-induced protein 8-like 2a Neighboring gene uncharacterized LOC137488453 Neighboring gene dihydrouridine synthase 3-like (S. cerevisiae) Neighboring gene mitochondrial transcription termination factor 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 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. Sema6D Regulates Zebrafish Vascular Patterning and Motor Neuronal Axon Growth in Spinal Cord. Sheng J, et al. Front Mol Neurosci, 2022. PMID 35465091, Free PMC Article
    2. Identification and characterization of zebrafish semaphorin 6D. Kimura M, et al. Biochem Biophys Res Commun, 2007 Nov 23. PMID 17897628
    3. Retinal Pigment Epithelium and Neural Retinal Progenitors Interact via Semaphorin 6D to Facilitate Optic Cup Morphogenesis. Cechmanek PB, et al. eNeuro, 2021 May-Jun. PMID 33811086, Free PMC Article
    4. γ-Aminobutyric acid receptor alpha 1 subunit loss of function causes genetic generalized epilepsy by impairing inhibitory network neurodevelopment. Samarut É, et al. Epilepsia, 2018 Nov. PMID 30324621
    5. Increased locomotor activity via regulation of GABAergic signalling in foxp2 mutant zebrafish-implications for neurodevelopmental disorders. Lüffe TM, et al. Transl Psychiatry, 2021 Oct 14. PMID 34650032, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 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
    		  
    acts_upstream_of_or_within axonogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within branching involved in blood vessel morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 optic cup morphogenesis involved in camera-type eye development 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
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    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-6C
    Names
    sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D

    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_212999.3 → NP_998164.3  semaphorin-6C

      Status: VALIDATED

      Source sequence(s)
      CU571385
      UniProtKB/TrEMBL
      A0A8M1PEE7, B8JMB1
      Related
      ENSDARP00000121171.1, ENSDART00000136361.2
      Conserved Domains (1) summary
      cl15693
      Location:64 → 523
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    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_007130.7 Reference GRCz11 Primary Assembly

      Range
      390297..417381
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068215104.1 → XP_068071205.1  semaphorin-6C isoform X1

    2. XM_068215105.1 → XP_068071206.1  semaphorin-6C isoform X2

    Nucleotide Protein Strain
    Heading Accession and Version

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