U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Protein

    • Showing Current items.

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

    Gene ID: 20350, updated on 27-Nov-2024

    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 AllianceGenome:MGI:1096347
    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
    Summary
    Enables chemorepellent activity. Involved in several processes, including nervous system development; semaphorin-plexin signaling pathway; and ventral trunk neural crest cell migration. Acts upstream of or within several processes, including axon guidance; negative regulation of axon extension involved in axon guidance; and trunk neural crest cell migration. Located in extracellular space. Is active in glutamatergic synapse. Is expressed in several structures, including alimentary system; brain; genitourinary system; respiratory system; and sensory organ. Orthologous to human SEMA3F (semaphorin 3F). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in lung adult (RPKM 77.6), limb E14.5 (RPKM 39.8) and 19 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Sema3f in Genome Data Viewer
    Location:
    9 F1; 9 58.91 cM
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (107558698..107587674, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (107681499..107710475, complement)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene solute carrier family 38, member 3 Neighboring gene G protein subunit alpha transducin 1 Neighboring gene predicted gene, 51690 Neighboring gene STARR-seq mESC enhancer starr_25187 Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:107637781-107637982 Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:107638598-107638781 Neighboring gene predicted gene, 34605 Neighboring gene RNA binding motif protein 5 Neighboring gene STARR-seq mESC enhancer starr_25188

    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 (1) 
    • Gene trapped (1) 
    • Targeted (9)  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 chemorepellent activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chemorepellent activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    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
    acts_upstream_of axon extension involved in axon guidance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of axon extension involved in axon guidance IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in axon extension involved in axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within axon guidance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within axon guidance ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    involved_in branchiomotor neuron axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in facial nerve structural organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within negative chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative chemotaxis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of axon extension involved in axon guidance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of axon extension involved in axon guidance IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in nerve development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in neural crest cell migration involved in autonomic nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of postsynapse organization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of postsynapse organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in semaphorin-plexin signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sympathetic ganglion development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sympathetic neuron projection extension IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sympathetic neuron projection guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in trigeminal nerve structural organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within trunk neural crest cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ventral trunk neural crest cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in extracellular space HDA PubMed 
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    semaphorin-3F
    Names
    semaphorin IV

    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_001311151.3NP_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)
      AC152718, AC162905
      Consensus CDS
      CCDS81069.1
      UniProtKB/Swiss-Prot
      E9QNC5, O88632, O88633
      Related
      ENSMUSP00000141865.2, ENSMUST00000192727.6
      Conserved Domains (3) 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)
      smart00423
      Location:547584
      PSI; domain found in Plexins, Semaphorins and Integrins
    2. NM_001379496.2NP_001366425.1  semaphorin-3F isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AC152718, AC162905
      Conserved Domains (3) summary
      cd11254
      Location:48517
      Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
      smart00423
      Location:516553
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:577666
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    3. NM_001405023.1NP_001391952.1  semaphorin-3F isoform 4 precursor

      Status: VALIDATED

      Source sequence(s)
      AC152718, AC162905
    4. NM_001405024.1NP_001391953.1  semaphorin-3F isoform 5 precursor

      Status: VALIDATED

      Source sequence(s)
      AC152718, AC162905
    5. NM_001405025.2NP_001391954.1  semaphorin-3F isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AC152718, AC162905
      UniProtKB/Swiss-Prot
      E9QNC5, O88632, O88633
    6. NM_011349.4NP_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)
      AC152718, AC162905
      Consensus CDS
      CCDS23505.1
      UniProtKB/Swiss-Prot
      O88632
      Related
      ENSMUSP00000079400.4, ENSMUST00000080560.9
      Conserved Domains (3) summary
      cd11254
      Location:48517
      Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
      smart00423
      Location:516553
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:577666
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3

    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_000075.7 Reference GRCm39 C57BL/6J

      Range
      107558698..107587674 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017313230.2XP_017168719.1  semaphorin-3F isoform X4

      Conserved Domains (3) summary
      smart00423
      Location:321358
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:383424
      Ig; Immunoglobulin domain
      cl15693
      Location:1322
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    2. XM_017313229.3XP_017168718.1  semaphorin-3F isoform X4

      Conserved Domains (3) summary
      smart00423
      Location:321358
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:383424
      Ig; Immunoglobulin domain
      cl15693
      Location:1322
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    RNA

    1. XR_379758.5 RNA Sequence

    2. XR_871078.4 RNA Sequence

    3. XR_379759.5 RNA Sequence