Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 20346, updated on 13-Jan-2019

    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
    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
    Expression
    Broad expression in limb E14.5 (RPKM 3.0), bladder adult (RPKM 3.0) and 16 other tissues See more
    Orthologs

    Genomic context

    See Sema3a in Genome Data Viewer
    Location:
    5; 5 A1
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 5 NC_000071.6 (13125370..13606234)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 5 NC_000071.5 (13399309..13602571)

    Chromosome 5 - NC_000071.6Genomic Context describing neighboring genes Neighboring gene predicted gene 6641 Neighboring gene cytochrome c, somatic pseudogene 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 FunctionsWhat's a GeneRIF?

    Variation

    Alleles

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

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    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 
    neuropilin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    neuropilin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    semaphorin receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    axonal fasciculation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    axonogenesis involved in innervation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    basal dendrite arborization IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    branchiomotor neuron axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    dendrite morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    dichotomous subdivision of terminal units involved in salivary gland branching IDA
    Inferred from Direct Assay
    more info
    PubMed 
    dichotomous subdivision of terminal units involved in salivary gland branching IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    facial nerve structural organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    facioacoustic ganglion development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    gonadotrophin-releasing hormone neuronal migration to the hypothalamus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    motor neuron axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    multicellular organism development IEA
    Inferred from Electronic Annotation
    more info
     
    negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative chemotaxis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of axon extension IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of axon extension IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of axon extension ISO
    Inferred from Sequence Orthology
    more info
     
    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 
    negative regulation of epithelial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of neuron projection development ISO
    Inferred from Sequence Orthology
    more info
     
    nerve development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    neural crest cell migration involved in autonomic nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neural crest cell migration involved in sympathetic nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neuron migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    olfactory bulb development ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of male gonad development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of neuron migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of neuron migration IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    regulation of axon extension involved in axon guidance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of axon extension involved in axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of heart rate 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 IGI
    Inferred from Genetic Interaction
    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 ganglion development 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
    axon IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    axon ISO
    Inferred from Sequence Orthology
    more info
     
    dendrite ISO
    Inferred from Sequence Orthology
    more info
     
    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 
    integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    semaphorin-3A
    Names
    collapsin-1
    sema D
    sema III
    semaphorin III
    semaphorin-D

    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_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
      O08665
      Related
      ENSMUSP00000092621.3, ENSMUST00000095012.9
      Conserved Domains (4) summary
      cd05871
      Location:581671
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00410
      Location:586664
      IG_like; Immunoglobulin like
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
    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
      O08665
      Related
      ENSMUSP00000128153.1, ENSMUST00000137798.7
      Conserved Domains (4) summary
      cd05871
      Location:581671
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00410
      Location:586664
      IG_like; Immunoglobulin like
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
    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
      O08665
      Related
      ENSMUSP00000030714.7, ENSMUST00000030714.7
      Conserved Domains (4) summary
      cd05871
      Location:581671
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00410
      Location:586664
      IG_like; Immunoglobulin like
      smart00423
      Location:516552
      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_000071.6 Reference GRCm38.p4 C57BL/6J

      Range
      13125370..13606234
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      See identical proteins and their annotated locations for XP_006503620.1

      UniProtKB/Swiss-Prot
      O08665
      Conserved Domains (4) summary
      cd05871
      Location:581671
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00410
      Location:586664
      IG_like; Immunoglobulin like
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
    2. XM_011240665.2XP_011238967.1  semaphorin-3A isoform X1

      See identical proteins and their annotated locations for XP_011238967.1

      UniProtKB/Swiss-Prot
      O08665
      Conserved Domains (4) summary
      cd05871
      Location:581671
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00410
      Location:586664
      IG_like; Immunoglobulin like
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
    3. XM_006503559.1XP_006503622.1  semaphorin-3A isoform X1

      See identical proteins and their annotated locations for XP_006503622.1

      UniProtKB/Swiss-Prot
      O08665
      Conserved Domains (4) summary
      cd05871
      Location:581671
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00410
      Location:586664
      IG_like; Immunoglobulin like
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
    4. XM_006503558.3XP_006503621.1  semaphorin-3A isoform X1

      See identical proteins and their annotated locations for XP_006503621.1

      UniProtKB/Swiss-Prot
      O08665
      Conserved Domains (4) summary
      cd05871
      Location:581671
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11249
      Location:26518
      Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
      smart00410
      Location:586664
      IG_like; Immunoglobulin like
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
    Support Center