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    Plxnd1 plexin D1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 312652, updated on 3-Dec-2024

    Summary

    Official Symbol
    Plxnd1provided by RGD
    Official Full Name
    plexin D1provided by RGD
    Primary source
    RGD:1310796
    See related
    EnsemblRapid:ENSRNOG00000025209 AllianceGenome:RGD:1310796
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable protein domain specific binding activity and semaphorin receptor activity. Predicted to be involved in several processes, including negative regulation of neuron apoptotic process; nervous system development; and positive regulation of axonogenesis. Predicted to act upstream of or within circulatory system development; dichotomous subdivision of terminal units involved in salivary gland branching; and kidney development. Predicted to be located in axon; cell body; and lamellipodium. Predicted to be part of semaphorin receptor complex. Predicted to be active in glutamatergic synapse and plasma membrane. Used to study transient cerebral ischemia. Orthologous to human PLXND1 (plexin D1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Lung (RPKM 183.7), Heart (RPKM 158.6) and 9 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Plxnd1 in Genome Data Viewer
    Location:
    4q42
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (150675377..150715706, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (149002786..149043097, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (147854309..147894170, complement)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene rhodopsin Neighboring gene H1.8 linker histone Neighboring gene transmembrane and coiled-coil domain family 1 Neighboring gene small RNA binding exonuclease protection factor La like 1 Neighboring gene WASH complex subunit 2C Neighboring gene ribosomal protein L9, pseudogene 19

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables protein domain specific binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables semaphorin receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables semaphorin receptor activity ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in angiogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within aorta development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within branching involved in blood vessel morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within cardiac septum development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within coronary vasculature development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within dichotomous subdivision of terminal units involved in salivary gland branching ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in endothelial cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within kidney development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of neuron apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within outflow tract morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of angiogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of cell shape 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 semaphorin-plexin signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in semaphorin-plexin signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in synapse assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synaptic target recognition ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in axon ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cell body ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
     
    located_in lamellipodium ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    part_of semaphorin receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001395052.2NP_001381981.2  plexin-D1 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/TrEMBL
      D4AA77
      Related
      ENSRNOP00000033101.6, ENSRNOT00000032158.8

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      150675377..150715706 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_005503232.2 RNA Sequence

    2. XR_005503233.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001107881.1: Suppressed sequence

      Description
      NM_001107881.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.