Format

Send to:

Choose Destination
    • Showing Current items.

    Sema3f sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [ Mus musculus (house mouse) ]

    Gene ID: 20350, updated on 8-Dec-2018

    Summary

    Official Symbol
    Sema3fprovided by MGI
    Official Full Name
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Fprovided by MGI
    Primary source
    MGI:MGI:1096347
    See related
    Ensembl:ENSMUSG00000034684
    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
    Sema4; Semak
    Expression
    Broad expression in lung adult (RPKM 77.6), limb E14.5 (RPKM 39.8) and 19 other tissues See more
    Orthologs

    Genomic context

    See Sema3f in Genome Data Viewer
    Location:
    9; 9 F1
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 9 NC_000075.6 (107681499..107710475, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (107583833..107612806, complement)

    Chromosome 9 - NC_000075.6Genomic Context describing neighboring genes Neighboring gene solute carrier family 38, member 3 Neighboring gene guanine nucleotide binding protein, alpha transducing 1 Neighboring gene predicted gene, 34605 Neighboring gene RNA binding motif protein 5

    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 FunctionsWhat's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from BioSystems

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    chemorepellent activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chemorepellent activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    neuropilin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    axon extension involved in axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    axon guidance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    axon guidance ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    branchiomotor neuron axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    facial nerve structural organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    locomotion IC
    Inferred by Curator
    more info
    PubMed 
    negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative chemotaxis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of axon extension involved in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of axon extension involved in axon guidance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of axon extension involved in axon guidance IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    nerve development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    neural crest cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neural crest cell migration involved in autonomic nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    regulation of postsynapse organization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of postsynapse organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    semaphorin-plexin signaling pathway involved in axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    semaphorin-plexin signaling pathway involved in neuron projection guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    sympathetic ganglion development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    sympathetic neuron projection extension IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    sympathetic neuron projection guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    trigeminal nerve structural organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    ventral trunk neural crest cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular space HDA PubMed 
    extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    semaphorin-3F
    Names
    semaphorin IV

    NCBI Reference Sequences (RefSeq)

    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_001311151.1NP_001298080.1  semaphorin-3F isoform 1 precursor

      See identical proteins and their annotated locations for NP_001298080.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AK053632, CF736303, CX566341
      Consensus CDS
      CCDS81069.1
      UniProtKB/Swiss-Prot
      O88632
      Related
      ENSMUSP00000141865.1, ENSMUST00000192727.5
      Conserved Domains (4) summary
      cd05871
      Location:609697
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11254
      Location:48548
      Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
      smart00410
      Location:612696
      IG_like; Immunoglobulin like
      smart00423
      Location:547584
      PSI; domain found in Plexins, Semaphorins and Integrins
    2. NM_011349.3NP_035479.2  semaphorin-3F isoform 2 precursor

      See identical proteins and their annotated locations for NP_035479.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AK053632
      Consensus CDS
      CCDS23505.1
      UniProtKB/Swiss-Prot
      O88632
      Related
      ENSMUSP00000079400.3, ENSMUST00000080560.8
      Conserved Domains (4) summary
      cd05871
      Location:578666
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11254
      Location:48517
      Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
      smart00410
      Location:581665
      IG_like; Immunoglobulin like
      smart00423
      Location:516553
      PSI; domain found in Plexins, Semaphorins and Integrins

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000075.6 Reference GRCm38.p4 C57BL/6J

      Range
      107681499..107710475 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017313228.1XP_017168717.1  semaphorin-3F isoform X3

      UniProtKB/Swiss-Prot
      O88632
      Conserved Domains (4) summary
      cd05871
      Location:609697
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11254
      Location:48548
      Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
      smart00410
      Location:612696
      IG_like; Immunoglobulin like
      smart00423
      Location:547584
      PSI; domain found in Plexins, Semaphorins and Integrins
    2. XM_006511676.3XP_006511739.1  semaphorin-3F isoform X4

      See identical proteins and their annotated locations for XP_006511739.1

      UniProtKB/Swiss-Prot
      O88632
      Conserved Domains (4) summary
      cd05871
      Location:578666
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11254
      Location:48517
      Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
      smart00410
      Location:581665
      IG_like; Immunoglobulin like
      smart00423
      Location:516553
      PSI; domain found in Plexins, Semaphorins and Integrins
    3. XM_017313230.1XP_017168719.1  semaphorin-3F isoform X5

    4. XM_017313229.1XP_017168718.1  semaphorin-3F isoform X5

    5. XM_017313227.1XP_017168716.1  semaphorin-3F isoform X2

    6. XM_017313226.1XP_017168715.1  semaphorin-3F isoform X1

    RNA

    1. XR_379758.3 RNA Sequence

    2. XR_871078.2 RNA Sequence

    3. XR_379759.3 RNA Sequence

    Support Center