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    plxnb1a plexin b1a [ Danio rerio (zebrafish) ]

    Gene ID: 561012, updated on 11-Apr-2024

    Summary

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    Official Symbol
    plxnb1aprovided by ZNC
    Official Full Name
    plexin b1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-050302-63
    See related
    Ensembl:ENSDARG00000075821 AllianceGenome:ZFIN:ZDB-GENE-050302-63
    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
    Also known as
    im:7054247; wu:fb83a09; si:ch211-220i18.5
    Summary
    Predicted to enable semaphorin receptor activity. Acts upstream of or within axon extension. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. Predicted to be part of semaphorin receptor complex. Predicted to be integral component of plasma membrane. Orthologous to human PLXNB1 (plexin B1). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    all
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    Genomic context

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    See plxnb1a in Genome Data Viewer
    Location:
    chromosome: 23
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (9938236..10137402, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 23 NC_007134.6 (10003852..10202425, complement)

    Chromosome 23 - NC_007134.7Genomic Context describing neighboring genes Neighboring gene si:ch211-220i18.4 Neighboring gene solute carrier family 16 member 7 Neighboring gene zgc:171775 Neighboring gene keratin 5

    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. Semaphorin 5A is a bifunctional axon guidance cue for axial motoneurons in vivo. Hilario JD, et al. Dev Biol, 2009 Feb 1. PMID 19059233
    2. BMP Signaling Interferes with Optic Chiasm Formation and Retinal Ganglion Cell Pathfinding in Zebrafish. Knickmeyer MD, et al. Int J Mol Sci, 2021 Apr 27. PMID 33925390, Free PMC Article
    3. Gene duplication followed by exon structure divergence substitutes for alternative splicing in zebrafish. Lambert MJ, et al. Gene, 2014 Aug 10. PMID 24942242
    4. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Lo J, et al. Genome Res, 2003 Mar. PMID 12618376, Free PMC Article
    5. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article

    See all (7) 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 semaphorin receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables semaphorin receptor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in axon extension IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within axon extension IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cell shape IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within semaphorin-plexin signaling pathway IEA
    Inferred from Electronic Annotation
    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
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of semaphorin receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    plexin-B1
    Names
    plexin b1

    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_007134.7 Reference GRCz11 Primary Assembly

      Range
      9938236..10137402 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009296674.3 → XP_009294949.1  plexin-B1 isoform X3

      UniProtKB/TrEMBL
      A0A8M3B5Y3
      Conserved Domains (6) summary
      smart00423
      Location:643 → 670
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd01180
      Location:847 → 938
      IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
      pfam01437
      Location:484 → 535
      PSI; Plexin repeat
      pfam08337
      Location:1358 → 1897
      Plexin_cytopl; Plexin cytoplasmic RasGAP domain
      cl15674
      Location:939 → 1028
      IPT; Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor ...
      cl15693
      Location:37 → 482
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. XM_001920948.7 → XP_001920983.4  plexin-B1 isoform X2

      UniProtKB/TrEMBL
      A0A8M1QKJ0
      Related
      ENSDARP00000138525.2, ENSDART00000166663.2
      Conserved Domains (6) summary
      smart00423
      Location:643 → 670
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd01180
      Location:1055 → 1146
      IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
      pfam01437
      Location:484 → 535
      PSI; Plexin repeat
      pfam08337
      Location:1561 → 2100
      Plexin_cytopl; Plexin cytoplasmic RasGAP domain
      cl15674
      Location:1147 → 1236
      IPT; Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor ...
      cl15693
      Location:37 → 482
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    3. XM_009296673.3 → XP_009294948.1  plexin-B1 isoform X1

      UniProtKB/TrEMBL
      A0A8M3AMN7
      Conserved Domains (6) summary
      smart00423
      Location:643 → 670
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd01180
      Location:1055 → 1146
      IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
      pfam01437
      Location:484 → 535
      PSI; Plexin repeat
      pfam08337
      Location:1566 → 2105
      Plexin_cytopl; Plexin cytoplasmic RasGAP domain
      cl15674
      Location:1147 → 1236
      IPT; Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor ...
      cl15693
      Location:37 → 482
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    Nucleotide Protein Strain
    Heading Accession and Version

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