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Sema3d semaphorin 3D [ Rattus norvegicus (Norway rat) ]

Gene ID: 246262, updated on 24-Jul-2025
Official Symbol
Sema3dprovided by RGD
Official Full Name
semaphorin 3Dprovided by RGD
Primary source
RGD:727939
See related
Ensembl:ENSRNOG00000007202 AllianceGenome:RGD:727939
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Predicted to be involved in several processes, including axon guidance; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to be active in extracellular space and plasma membrane. Orthologous to human SEMA3D (semaphorin 3D). [provided by Alliance of Genome Resources, Apr 2025]
Expression
Biased expression in Spleen (RPKM 149.7), Kidney (RPKM 92.6) and 8 other tissues See more
Orthologs
human mouse all
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See Sema3d in Genome Data Viewer
Location:
4q12
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (23271815..23460971, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (22316769..22505930, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (19224378..19413519, complement)

Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134486718 Neighboring gene uncharacterized LOC134486719 Neighboring gene U6 spliceosomal RNA Neighboring gene MLV-related proviral Env polyprotein-like, pseudogene 4

Go to nucleotide: Graphics FASTA GenBank

  • 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

Related articles in PubMed

  1. Expression of Sema3D in subsets of neurons in the developing dorsal root ganglia of the rat. Takahashi K, et al. Neurosci Lett, 2009 May 8. PMID 19429098
  2. Identification and tissue-specific expression of a novel isoform of Semaphorin 3D. Takahashi K, et al. Biochim Biophys Acta, 2009 May. PMID 19345252
  3. FMRP recruitment of β-catenin to the translation pre-initiation complex represses translation. Ehyai S, et al. EMBO Rep, 2018 Dec. PMID 30361391, Free PMC Article
  4. Extracellular matrix secretion by cardiac fibroblasts: role of microRNA-29b and microRNA-30c. Abonnenc M, et al. Circ Res, 2013 Oct 25. PMID 24006456
  5. 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

What's a GeneRIF?
  1. Sema3D may regulate the axonal navigation of the large diameter DRG neurons.
    Title: Expression of Sema3D in subsets of neurons in the developing dorsal root ganglia of the rat.
  2. Gene regulation, via an alternative splicing mechanism, affects not only the tissue-specificity of Sema 3D expression, but also the distance over which it can act.
    Title: Identification and tissue-specific expression of a novel isoform of Semaphorin 3D.
Submit: New GeneRIF Correction
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by RGD

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
  
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of developmental process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of multicellular organismal process IEA
Inferred from Electronic Annotation
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 regulation of anatomical structure morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of multicellular organismal development IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of plasma membrane bounded cell projection organization IEA
Inferred from Electronic Annotation
more info
  
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
Preferred Names
semaphorin-3D
Names
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D
semaphorin, homolog of the avian Sema3D

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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_001104633.1 → NP_001098103.1  semaphorin-3D

    Status: PROVISIONAL

    Source sequence(s)
    JAXUCZ010000004
    UniProtKB/TrEMBL
    A7M6E9, F1MAG8
    Related
    ENSRNOP00000009489.5, ENSRNOT00000009489.8
    Conserved Domains (3) summary
    cd11252
    Location:61 → 534
    Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
    smart00423
    Location:533 → 570
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:595 → 686
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3

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
    23271815..23460971 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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