Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 363142, updated on 21-Jul-2018

    Summary

    Official Symbol
    Sema3bprovided by RGD
    Official Full Name
    semaphorin 3Bprovided by RGD
    Primary source
    RGD:1310079
    See related
    Ensembl:ENSRNOG00000016512
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Expression
    Biased expression in Kidney (RPKM 114.3), Lung (RPKM 106.8) and 8 other tissues See more
    Orthologs

    Genomic context

    See Sema3b in Genome Data Viewer
    Location:
    8q32
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (116353791..116362655, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 8 NC_005107.3 (115710050..115719431, complement)

    Chromosome 8 - NC_005107.4Genomic Context describing neighboring genes Neighboring gene interferon-related developmental regulator 2 Neighboring gene leucine-rich single-pass membrane protein 2 Neighboring gene G protein subunit alpha i2 Neighboring gene solute carrier family 38, member 3

    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

    Pathways from BioSystems

    • Axon guidance, organism-specific biosystem (from KEGG)
      Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
    • Axon guidance, conserved biosystem (from KEGG)
      Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    neuropilin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of axon extension involved in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    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-3B
    Names
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B

    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_001079942.1NP_001073411.1  semaphorin-3B precursor

      See identical proteins and their annotated locations for NP_001073411.1

      Status: PROVISIONAL

      Source sequence(s)
      BC129103
      UniProtKB/TrEMBL
      D3ZHJ3
      Related
      ENSRNOP00000060214.1, ENSRNOT00000066296.1
      Conserved Domains (3) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005107.4 Reference Rnor_6.0 Primary Assembly

      Range
      116353791..116362655 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017595747.1XP_017451236.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3
      Conserved Domains (3) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    2. XM_006243810.3XP_006243872.1  semaphorin-3B isoform X1

      See identical proteins and their annotated locations for XP_006243872.1

      UniProtKB/TrEMBL
      D3ZHJ3
      Conserved Domains (3) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    3. XM_017595748.1XP_017451237.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      D3ZHJ3
      Conserved Domains (3) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    Alternate Rn_Celera

    Genomic

    1. AC_000076.1 Alternate Rn_Celera

      Range
      107578526..107585547 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Support Center