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    Sema3d sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D [ Mus musculus (house mouse) ]

    Gene ID: 108151, updated on 9-Dec-2024

    Summary

    Official Symbol
    Sema3dprovided by MGI
    Official Full Name
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Dprovided by MGI
    Primary source
    MGI:MGI:1860118
    See related
    Ensembl:ENSMUSG00000040254 AllianceGenome:MGI:1860118
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    4631426B19Rik
    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. Located in extracellular space. Is expressed in several structures, including alimentary system; foot mesenchyme; intraembryonic coelom; nervous system; and sensory organ. Orthologous to human SEMA3D (semaphorin 3D). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in limb E14.5 (RPKM 4.3), bladder adult (RPKM 3.0) and 18 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Sema3d in Genome Data Viewer
    Location:
    5 A1; 5 3.97 cM
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (12433133..12638920)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (12383161..12588953)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_12440 Neighboring gene predicted gene, 54301 Neighboring gene 2-cell-stage, variable group, member 3-like pseudogene Neighboring gene VISTA enhancer mm832 Neighboring gene predicted gene 8925 Neighboring gene STARR-seq mESC enhancer starr_12442 Neighboring gene STARR-seq mESC enhancer starr_12443 Neighboring gene predicted gene 42580 Neighboring gene STARR-seq mESC enhancer starr_12444 Neighboring gene STARR-seq mESC enhancer starr_12445 Neighboring gene STARR-seq mESC enhancer starr_12446 Neighboring gene STARR-seq mESC enhancer starr_12448 Neighboring gene STARR-seq mESC enhancer starr_12449 Neighboring gene STARR-seq mESC enhancer starr_12450 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (5)  1 citation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    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 cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in nervous system development 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 semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in extracellular space HDA PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in plasma membrane 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_028882.4NP_083158.3  semaphorin-3D precursor

      See identical proteins and their annotated locations for NP_083158.3

      Status: VALIDATED

      Source sequence(s)
      AK052671, AK163828, CF746948
      Consensus CDS
      CCDS39013.1
      UniProtKB/Swiss-Prot
      Q8BH34
      UniProtKB/TrEMBL
      Q8BMF6
      Related
      ENSMUSP00000030868.7, ENSMUST00000030868.11
      Conserved Domains (3) summary
      cd05871
      Location:596686
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11252
      Location:61534
      Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
      smart00423
      Location:533570
      PSI; domain found in Plexins, Semaphorins and Integrins

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      12433133..12638920
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030254046.2XP_030109906.1  semaphorin-3D isoform X1

      UniProtKB/Swiss-Prot
      Q8BH34
      UniProtKB/TrEMBL
      Q8BMF6
      Conserved Domains (3) summary
      cd05871
      Location:596686
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11252
      Location:61534
      Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
      smart00423
      Location:533570
      PSI; domain found in Plexins, Semaphorins and Integrins