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    Sema3a sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A [ Mus musculus (house mouse) ]

    Gene ID: 20346, updated on 9-Dec-2024

    Summary

    Official Symbol
    Sema3aprovided by MGI
    Official Full Name
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Aprovided by MGI
    Primary source
    MGI:MGI:107558
    See related
    Ensembl:ENSMUSG00000028883 AllianceGenome:MGI:107558
    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
    SemD; SEMA1; Semad; coll-1; Hsema-I
    Summary
    Enables chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Involved in several processes, including nervous system development; positive regulation of male gonad development; and ventral trunk neural crest cell migration. Acts upstream of or within several processes, including dichotomous subdivision of terminal units involved in salivary gland branching; negative regulation of axon extension involved in axon guidance; and neuron projection development. Located in extracellular space. Is active in cerebellar climbing fiber to Purkinje cell synapse. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; metanephros; and sensory organ. Human ortholog(s) of this gene implicated in hypogonadotropic hypogonadism 16 with or without anosmia. Orthologous to human SEMA3A (semaphorin 3A). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in limb E14.5 (RPKM 3.0), bladder adult (RPKM 3.0) and 16 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Sema3a in Genome Data Viewer
    Location:
    5 A1; 5 4.31 cM
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (13174789..13653453)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (13124822..13603485)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene predicted gene 6641 Neighboring gene cytochrome c, somatic pseudogene Neighboring gene predicted gene, 52804 Neighboring gene STARR-seq mESC enhancer starr_12452 Neighboring gene STARR-seq mESC enhancer starr_12453 Neighboring gene STARR-seq mESC enhancer starr_12455 Neighboring gene STARR-seq mESC enhancer starr_12456 Neighboring gene anaphase-promoting complex subunit 5 pseudogene Neighboring gene predicted gene 6647

    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)

    Pathways from PubChem

    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 neuropilin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables neuropilin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables semaphorin receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    acts_upstream_of axon extension IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of axon extension IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    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 
    acts_upstream_of_or_within axon guidance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within axonal fasciculation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in axonogenesis involved in innervation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in basal dendrite arborization IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in branchiomotor neuron axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within dendrite morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within dichotomous subdivision of terminal units involved in salivary gland branching IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within dichotomous subdivision of terminal units involved in salivary gland branching IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of epithelial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in facial nerve structural organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in facioacoustic ganglion development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in gonadotrophin-releasing hormone neuronal migration to the hypothalamus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in maintenance of synapse structure IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in maintenance of synapse structure IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in motor neuron axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in motor neuron axon guidance 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 IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of axon extension IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of axon extension IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in negative regulation of axon extension ISO
    Inferred from Sequence Orthology
    more info
     
    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 
    acts_upstream_of_or_within negative regulation of epithelial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of neuron projection development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in nerve development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within nervous system development IGI
    Inferred from Genetic Interaction
    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 neural crest cell migration involved in sympathetic nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuron migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in olfactory bulb development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in olfactory bulb development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of male gonad development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of neuron migration IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in regulation of axon extension involved in axon guidance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of axon extension involved in axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of heart rate IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within semaphorin-plexin signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    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 synaptic target recognition IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in synaptic target recognition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in trigeminal ganglion development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in trigeminal nerve structural organization 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
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in axon ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in cerebellar climbing fiber to Purkinje cell synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cerebellar climbing fiber to Purkinje cell synapse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in dendrite ISO
    Inferred from Sequence Orthology
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    located_in extracellular space HDA PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in glutamatergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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-3A
    Names
    collapsin-1
    sema D
    sema III
    semaphorin III
    semaphorin-D

    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_001243072.1NP_001230001.1  semaphorin-3A precursor

      See identical proteins and their annotated locations for NP_001230001.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC022368, BC090844
      Consensus CDS
      CCDS19092.1
      UniProtKB/Swiss-Prot
      E9QK85, O08665, Q5BL08, Q62180, Q62215
      UniProtKB/TrEMBL
      A0A803Z7F8
      Related
      ENSMUSP00000092621.5, ENSMUST00000095012.11
      Conserved Domains (3) summary
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:580671
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    2. NM_001243073.1NP_001230002.1  semaphorin-3A precursor

      See identical proteins and their annotated locations for NP_001230002.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC022368, AK140817
      Consensus CDS
      CCDS19092.1
      UniProtKB/Swiss-Prot
      E9QK85, O08665, Q5BL08, Q62180, Q62215
      UniProtKB/TrEMBL
      A0A803Z7F8
      Related
      ENSMUSP00000128153.3, ENSMUST00000137798.10
      Conserved Domains (3) summary
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:580671
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    3. NM_009152.4NP_033178.2  semaphorin-3A precursor

      See identical proteins and their annotated locations for NP_033178.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC022368, AC121125, BC057588
      Consensus CDS
      CCDS19092.1
      UniProtKB/Swiss-Prot
      E9QK85, O08665, Q5BL08, Q62180, Q62215
      UniProtKB/TrEMBL
      A0A803Z7F8
      Related
      ENSMUSP00000030714.9, ENSMUST00000030714.9
      Conserved Domains (3) summary
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:580671
      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_000071.7 Reference GRCm39 C57BL/6J

      Range
      13174789..13653453
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006503557.5XP_006503620.2  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      E9QK85, O08665, Q5BL08, Q62180, Q62215
      UniProtKB/TrEMBL
      A0A803Z7F8
      Conserved Domains (3) summary
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:580671
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    2. XM_011240665.4XP_011238967.2  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      E9QK85, O08665, Q5BL08, Q62180, Q62215
      UniProtKB/TrEMBL
      A0A803Z7F8
      Conserved Domains (3) summary
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:580671
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    3. XM_036164936.1XP_036020829.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      E9QK85, O08665, Q5BL08, Q62180, Q62215
      UniProtKB/TrEMBL
      A0A803Z7F8
      Conserved Domains (3) summary
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:580671
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    4. XM_036164937.1XP_036020830.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      E9QK85, O08665, Q5BL08, Q62180, Q62215
      UniProtKB/TrEMBL
      A0A803Z7F8
      Conserved Domains (3) summary
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:580671
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    5. XM_006503559.3XP_006503622.2  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      E9QK85, O08665, Q5BL08, Q62180, Q62215
      UniProtKB/TrEMBL
      A0A803Z7F8
      Conserved Domains (3) summary
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:580671
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    6. XM_036164935.1XP_036020828.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      E9QK85, O08665, Q5BL08, Q62180, Q62215
      UniProtKB/TrEMBL
      A0A803Z7F8
      Conserved Domains (3) summary
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:580671
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    7. XM_006503558.5XP_006503621.2  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      E9QK85, O08665, Q5BL08, Q62180, Q62215
      UniProtKB/TrEMBL
      A0A803Z7F8
      Conserved Domains (3) summary
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:580671
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3