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    ntn1b netrin 1b [ Danio rerio (zebrafish) ]

    Gene ID: 30192, updated on 9-Dec-2024

    Summary

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    Official Symbol
    ntn1bprovided by ZNC
    Official Full Name
    netrin 1bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-990415-168
    See related
    Ensembl:ENSDARG00000022531 AllianceGenome:ZFIN:ZDB-GENE-990415-168
    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
    net1; ntn1
    Summary
    Involved in negative regulation of extrinsic apoptotic signaling pathway in absence of ligand. Acts upstream of or within neuron projection development and regulation of axon extension. Predicted to be located in cytoplasm and extracellular region. Predicted to be active in basement membrane. Is expressed in several structures, including central nervous system; forebrain neural rod; head; hypochord; and neural plate. Human ortholog(s) of this gene implicated in congenital mirror movement disorder. Orthologous to human NTN1 (netrin 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See ntn1b in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (25708742..25813789, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (25578204..25683272, complement)

    Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene ubiquitin specific peptidase 43b Neighboring gene uncharacterized LOC101886214 Neighboring gene uncharacterized LOC137490596 Neighboring gene uncharacterized LOC137490593 Neighboring gene phosphoinositide-3-kinase, regulatory subunit 6b Neighboring gene major facilitator superfamily domain containing 6-like

    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. Pioneer Axons Utilize a Dcc Signaling-Mediated Invasion Brake to Precisely Complete Their Pathfinding Odyssey. Kikel-Coury NL, et al. J Neurosci, 2021 Aug 4. PMID 34131031, Free PMC Article
    2. A floor plate enhancer of the zebrafish netrin1 gene requires Cyclops (Nodal) signalling and the winged helix transcription factor FoxA2. Rastegar S, et al. Dev Biol, 2002 Dec 1. PMID 12453456
    3. accordion, a zebrafish behavioral mutant, has a muscle relaxation defect due to a mutation in the ATPase Ca2+ pump SERCA1. Hirata H, et al. Development, 2004 Nov. PMID 15469975
    4. An amphioxus netrin gene is expressed in midline structures during embryonic and larval development. Shimeld S. Dev Genes Evol, 2000 Jul. PMID 11180840
    5. Netrin/DCC signaling controls contralateral dendrites of octavolateralis efferent neurons. Suli A, et al. J Neurosci, 2006 Dec 20. PMID 17182783, Free PMC Article

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Careful phenotyping of patients combined with molecular and functional studies in zebrafish identifed netrin-1 as a potential shared genetic factor for cardiac and thyroid congenital defects.
      Title: Functional zebrafish studies based on human genotyping point to netrin-1 as a link between aberrant cardiovascular development and thyroid dysgenesis.
    2. These findings implicate Netrins as the only known attractants for olfactory sensory neurons.
      Title: Netrin/DCC signaling guides olfactory sensory axons to their correct location in the olfactory bulb.
    3. floor plate enhancer of netrin 1 requires Cyclops signalling and the winged helix transcription factor FoxA2
      Title: A floor plate enhancer of the zebrafish netrin1 gene requires Cyclops (Nodal) signalling and the winged helix transcription factor FoxA2.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in animal organ morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within anterior commissure morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within anterior commissure morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within central nervous system projection neuron axonogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in dendrite development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within dendrite development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in motor neuron axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of extrinsic apoptotic signaling pathway in absence of ligand 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 regulation of axon extension IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in tissue development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in basement membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    netrin-1b
    Names
    etID309922.3

    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_130998.1 → NP_571073.1  netrin-1b precursor

      See identical proteins and their annotated locations for NP_571073.1

      Status: PROVISIONAL

      Source sequence(s)
      AF017420
      UniProtKB/TrEMBL
      O42203
      Related
      ENSDARP00000038885.4, ENSDART00000039482.5
      Conserved Domains (4) summary
      smart00136
      Location:45 → 282
      LamNT; Laminin N-terminal domain (domain VI)
      cd00055
      Location:283 → 328
      EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...
      cd03579
      Location:486 → 602
      NTR_netrin-1_like; NTR domain, Netrin-1-like subfamily; The C-terminal NTR domain of netrins is also called domain C in the context of C. elegans netrin UNC-6. Netrins are secreted proteins that function as tropic cues in the direction of axon growth and cell migration ...
      pfam00053
      Location:403 → 440
      Laminin_EGF; Laminin EGF domain

    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_007114.7 Reference GRCz11 Primary Assembly

      Range
      25708742..25813789 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005171552.5 → XP_005171609.1  netrin-1b isoform X1

      See identical proteins and their annotated locations for XP_005171609.1

      UniProtKB/TrEMBL
      A0A8M2BJC5, F1QUK5
      Related
      ENSDARP00000134866.1, ENSDART00000169706.3
      Conserved Domains (4) summary
      smart00136
      Location:45 → 282
      LamNT; Laminin N-terminal domain (domain VI)
      cd00055
      Location:402 → 450
      EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...
      cd03579
      Location:486 → 602
      NTR_netrin-1_like; NTR domain, Netrin-1-like subfamily; The C-terminal NTR domain of netrins is also called domain C in the context of C. elegans netrin UNC-6. Netrins are secreted proteins that function as tropic cues in the direction of axon growth and cell migration ...
      pfam00053
      Location:340 → 389
      Laminin_EGF; Laminin EGF domain

    2. XM_005171551.5 → XP_005171608.1  netrin-1b isoform X1

      See identical proteins and their annotated locations for XP_005171608.1

      UniProtKB/TrEMBL
      A0A8M2BJC5, F1QUK5
      Conserved Domains (4) summary
      smart00136
      Location:45 → 282
      LamNT; Laminin N-terminal domain (domain VI)
      cd00055
      Location:402 → 450
      EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...
      cd03579
      Location:486 → 602
      NTR_netrin-1_like; NTR domain, Netrin-1-like subfamily; The C-terminal NTR domain of netrins is also called domain C in the context of C. elegans netrin UNC-6. Netrins are secreted proteins that function as tropic cues in the direction of axon growth and cell migration ...
      pfam00053
      Location:340 → 389
      Laminin_EGF; Laminin EGF domain
    Nucleotide Protein
    Heading Accession and Version

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