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    Sema6b semaphorin 6B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 84609, updated on 27-Dec-2024

    Summary

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    Official Symbol
    Sema6bprovided by RGD
    Official Full Name
    semaphorin 6Bprovided by RGD
    Primary source
    RGD:69278
    See related
    EnsemblRapid:ENSRNOG00000045998 AllianceGenome:RGD:69278
    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 nervous system development; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to be located in membrane. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in progressive myoclonus epilepsy. Orthologous to human SEMA6B (semaphorin 6B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 54.3), Spleen (RPKM 15.9) and 6 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sema6b in Genome Data Viewer
    Location:
    9q11
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (1038103..1055063, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (950939..967905, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (10934273..10951252)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene perilipin 5 Neighboring gene leucine-rich alpha-2-glycoprotein 1 Neighboring gene TNF alpha induced protein 8 like 1 Neighboring gene uncharacterized LOC134480469 Neighboring gene myeloid-derived growth factor Neighboring gene dipeptidyl peptidase 9

    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
    • 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. Molecular cloning of a novel member of semaphorin family genes, semaphorin Z. Kikuchi K, et al. Brain Res Mol Brain Res, 1997 Nov. PMID 9427525
    2. Plexin-a4 mediates axon-repulsive activities of both secreted and transmembrane semaphorins and plays roles in nerve fiber guidance. Suto F, et al. J Neurosci, 2005 Apr 6. PMID 15814794, 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 semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables semaphorin receptor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables semaphorin receptor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in axon guidance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axon guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in central nervous system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in central nervous system development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in hippocampus development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in hippocampus development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in hippocampus development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    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 semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    semaphorin-6B
    Names
    sema Z
    sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B
    semaphorin-Z

    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_053471.4 → NP_445923.1  semaphorin-6B precursor

      See identical proteins and their annotated locations for NP_445923.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      O70141
      UniProtKB/TrEMBL
      A0A8L2QYG3
      Related
      ENSRNOP00000067668.3, ENSRNOT00000070794.3
      Conserved Domains (3) summary
      cd11267
      Location:58 → 526
      Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
      PHA03247
      Location:698 → 885
      PHA03247; large tegument protein UL36; Provisional
      pfam01437
      Location:527 → 556
      PSI; Plexin repeat

    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_086027.1 Reference GRCr8

      Range
      1038103..1055063 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006244349.5 → XP_006244411.1  semaphorin-6B isoform X2

      See identical proteins and their annotated locations for XP_006244411.1

      UniProtKB/Swiss-Prot
      O70141
      UniProtKB/TrEMBL
      A0A8L2QYG3
      Conserved Domains (3) summary
      cd11267
      Location:58 → 526
      Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
      PHA03247
      Location:698 → 885
      PHA03247; large tegument protein UL36; Provisional
      pfam01437
      Location:527 → 556
      PSI; Plexin repeat

    2. XM_006244348.5 → XP_006244410.1  semaphorin-6B isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZKZ1, A6KQZ7
      Related
      ENSRNOP00000078468.1, ENSRNOT00000107355.2
      Conserved Domains (2) summary
      cd11267
      Location:128 → 596
      Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
      pfam01437
      Location:597 → 626
      PSI; Plexin repeat
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O70141.1 GenPept UniProtKB/Swiss-Prot:O70141

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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