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    Sema3b semaphorin 3B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363142, updated on 12-Oct-2024

    Summary

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    Official Symbol
    Sema3bprovided by RGD
    Official Full Name
    semaphorin 3Bprovided by RGD
    Primary source
    RGD:1310079
    See related
    EnsemblRapid:ENSRNOG00000016512 AllianceGenome:RGD:1310079
    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
    Summary
    Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Predicted to be involved in several processes, including generation of neurons; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Orthologous to human SEMA3B (semaphorin 3B). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Kidney (RPKM 114.3), Lung (RPKM 106.8) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sema3b in Genome Data Viewer
    Location:
    8q32
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (117150307..117161570, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (108271663..108280326, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (116353791..116362655, complement)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene hyaluronidase 1 Neighboring gene N(alpha)-acetyltransferase 80, NatH catalytic subunit Neighboring gene hyaluronidase 3 Neighboring gene interferon-related developmental regulator 2 Neighboring gene leucine-rich single-pass membrane protein 2 Neighboring gene uncharacterized LOC120094260 Neighboring gene G protein subunit alpha i2 Neighboring gene solute carrier family 38, member 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

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    Related articles in PubMed

    1. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. Prunotto M, et al. J Proteomics, 2013 Apr 26. PMID 23376485
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    		  
    Process Evidence Code Pubs
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of plasma membrane bounded cell projection organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    semaphorin-3B
    Names
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B

    NCBI Reference Sequences (RefSeq)

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    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_001079942.2 → NP_001073411.1  semaphorin-3B precursor

      See identical proteins and their annotated locations for NP_001073411.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      D3ZHJ3
      Related
      ENSRNOP00000060214.1, ENSRNOT00000066296.3
      Conserved Domains (3) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. NM_001433902.1 → NP_001420831.1  semaphorin-3B precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008

    3. NM_001433903.1 → NP_001420832.1  semaphorin-3B precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008

    4. NM_001433904.1 → NP_001420833.1  semaphorin-3B precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008

    5. NM_001433905.1 → NP_001420834.1  semaphorin-3B precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008

    6. NM_001433906.1 → NP_001420835.1  semaphorin-3B precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008

    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
      117150307..117161570 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063265824.1 → XP_063121894.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3

    2. XM_063265834.1 → XP_063121904.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3

    3. XM_063265833.1 → XP_063121903.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3

    4. XM_063265832.1 → XP_063121902.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3

    5. XM_063265830.1 → XP_063121900.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3

    6. XM_063265825.1 → XP_063121895.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3

    7. XM_063265828.1 → XP_063121898.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3

    8. XM_017595747.2 → XP_017451236.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3
      Conserved Domains (3) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    9. XM_063265826.1 → XP_063121896.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3

    10. XM_063265835.1 → XP_063121905.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3

    11. XM_063265829.1 → XP_063121899.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3

    12. XM_063265827.1 → XP_063121897.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3
    Nucleotide Protein Strain
    Heading Accession and Version

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