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    Sema3f semaphorin 3F [ Rattus norvegicus (Norway rat) ]

    Gene ID: 315996, updated on 9-Dec-2024

    Summary

    Official Symbol
    Sema3fprovided by RGD
    Official Full Name
    semaphorin 3Fprovided by RGD
    Primary source
    RGD:1308514
    See related
    EnsemblRapid:ENSRNOG00000017704 AllianceGenome:RGD:1308514
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    SemaIV
    Summary
    Predicted to enable chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Predicted to be involved in several processes, including nervous system development; semaphorin-plexin signaling pathway; and ventral trunk neural crest cell migration. Predicted to act upstream of or within negative regulation of axon extension involved in axon guidance and trunk neural crest cell migration. Predicted to be active in glutamatergic synapse and plasma membrane. Orthologous to human SEMA3F (semaphorin 3F). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 82.3), Kidney (RPKM 34.3) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Sema3f in Genome Data Viewer
    Location:
    8q32
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (117236269..117265206, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (108357629..108386569, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (116439996..116469915, complement)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene solute carrier family 38, member 3 Neighboring gene uncharacterized LOC134480231 Neighboring gene G protein subunit alpha transducin 1 Neighboring gene RNA binding motif protein 5 Neighboring gene RNA binding motif protein 6 Neighboring gene cofilin 1 like 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chemorepellent activity  
    enables chemorepellent activity  
    enables neuropilin binding  
    enables semaphorin receptor binding  
    Process Evidence Code Pubs
    acts_upstream_of axon extension involved in axon guidance  
    involved_in axon extension involved in axon guidance  
    involved_in axon guidance  
    acts_upstream_of_or_within axon guidance  
    involved_in branchiomotor neuron axon guidance  
    involved_in facial nerve structural organization  
    involved_in negative chemotaxis  
    acts_upstream_of_or_within negative chemotaxis  
    acts_upstream_of_or_within negative regulation of axon extension involved in axon guidance  
    involved_in nerve development  
    involved_in neural crest cell migration  
    involved_in neural crest cell migration involved in autonomic nervous system development  
    involved_in positive regulation of cell migration  
    involved_in regulation of postsynapse organization  
    involved_in semaphorin-plexin signaling pathway  
    involved_in semaphorin-plexin signaling pathway  
    involved_in sympathetic ganglion development  
    involved_in sympathetic neuron projection extension  
    involved_in sympathetic neuron projection guidance  
    involved_in trigeminal nerve structural organization  
    acts_upstream_of_or_within trunk neural crest cell migration  
    involved_in ventral trunk neural crest cell migration  
    Component Evidence Code Pubs
    is_active_in glutamatergic synapse  
    is_active_in plasma membrane  

    General protein information

    Preferred Names
    semaphorin-3F
    Names
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F
    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_001413830.1 → NP_001400759.1  semaphorin-3F precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A6I309, D3ZGX9
      Related
      ENSRNOP00000024193.5, ENSRNOT00000024193.7

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086026.1 Reference GRCr8

      Range
      117236269..117265206 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063265627.1 → XP_063121697.1  semaphorin-3F isoform X4

      UniProtKB/TrEMBL
      A0A0G2K0S6, A6I308
      Related
      ENSRNOP00000100452.1, ENSRNOT00000144059.1
    2. XM_039081590.2 → XP_038937518.1  semaphorin-3F isoform X2

      UniProtKB/TrEMBL
      A6I309, D3ZGX9
      Conserved Domains (3) summary
      cd11254
      Location:48 → 548
      Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
      smart00423
      Location:547 → 584
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:608 → 697
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    3. XM_039081591.2 → XP_038937519.1  semaphorin-3F isoform X3

      Related
      ENSRNOP00000071565.3, ENSRNOT00000085915.3
      Conserved Domains (3) summary
      cd11254
      Location:65 → 534
      Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
      smart00423
      Location:533 → 570
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:594 → 683
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    4. XM_039081588.1 → XP_038937516.1  semaphorin-3F isoform X1

      Conserved Domains (3) summary
      cd11254
      Location:65 → 565
      Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
      smart00423
      Location:564 → 601
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:625 → 714
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    5. XM_039081592.2 → XP_038937520.1  semaphorin-3F isoform X5

      Conserved Domains (3) summary
      smart00423
      Location:384 → 421
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:445 → 534
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
      cl15693
      Location:21 → 385
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    6. XM_039081593.2 → XP_038937521.1  semaphorin-3F isoform X6

      Conserved Domains (1) summary
      cl15693
      Location:65 → 496
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    RNA

    1. XR_005487847.2 RNA Sequence

      Related
      ENSRNOT00000165502.1
    2. XR_005487846.2 RNA Sequence

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