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    Sema6c semaphorin 6C [ Rattus norvegicus (Norway rat) ]

    Gene ID: 29744, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Sema6cprovided by RGD
    Official Full Name
    semaphorin 6Cprovided by RGD
    Primary source
    RGD:3659
    See related
    Ensembl:ENSRNOG00000021101 AllianceGenome:RGD:3659
    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
    Summary
    Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Involved in axon guidance. Predicted to be located in cell surface and cytoplasm. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Orthologous to human SEMA6C (semaphorin 6C). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Muscle (RPKM 75.7), Testes (RPKM 20.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sema6c in Genome Data Viewer
    Location:
    2q34
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (185422636..185436237)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (182733635..182750066)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (196330777..196347218)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene sodium channel modifier 1 Neighboring gene LysM domain containing 1 Neighboring gene TNF alpha induced protein 8 like 2 Neighboring gene uncharacterized LOC120100877 Neighboring gene GA binding protein transcription factor subunit beta 2 Neighboring gene MLLT11, transcription factor 7 cofactor

    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. Cloning and characterization of a novel class VI semaphorin, semaphorin Y. Kikuchi K, et al. Mol Cell Neurosci, 1999 Jan. PMID 10049528
    2. Identification, characterization, and functional study of the two novel human members of the semaphorin gene family. Qu X, et al. J Biol Chem, 2002 Sep 20. PMID 12110693
    3. PlexinA1 signaling directs the segregation of proprioceptive sensory axons in the developing spinal cord. Yoshida Y, et al. Neuron, 2006 Dec 7. PMID 17145500, Free PMC Article
    4. 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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    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of axon extension ISO
    Inferred from Sequence Orthology
    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 cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    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-6C
    Names
    Sema Y
    sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C
    semaphorin-Y

    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_017308.1 → NP_059004.1  semaphorin-6C precursor

      See identical proteins and their annotated locations for NP_059004.1

      Status: PROVISIONAL

      Source sequence(s)
      AB000817
      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Related
      ENSRNOP00000050221.1, ENSRNOT00000050914.4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    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_086020.1 Reference GRCr8

      Range
      185422636..185436237
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017590804.3 → XP_017446293.1  semaphorin-6C isoform X1

      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. XM_017590800.3 → XP_017446289.1  semaphorin-6C isoform X1

      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    3. XM_039102126.2 → XP_038958054.1  semaphorin-6C isoform X1

      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    4. XM_006232858.5 → XP_006232920.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_006232920.1

      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    5. XM_063281681.1 → XP_063137751.1  semaphorin-6C isoform X2

      UniProtKB/TrEMBL
      A6K2W1

    6. XM_008761293.4 → XP_008759515.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_008759515.1

      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    7. XM_006232861.5 → XP_006232923.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_006232923.1

      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    8. XM_017590802.3 → XP_017446291.1  semaphorin-6C isoform X1

      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    9. XM_017590806.3 → XP_017446295.1  semaphorin-6C isoform X1

      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    10. XM_017590807.3 → XP_017446296.1  semaphorin-6C isoform X1

      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    11. XM_017590809.3 → XP_017446298.1  semaphorin-6C isoform X1

      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    12. XM_039102128.2 → XP_038958056.1  semaphorin-6C isoform X1

      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    13. XM_017590808.3 → XP_017446297.1  semaphorin-6C isoform X1

      UniProtKB/Swiss-Prot
      Q9WTL3, Q9WTM6
      UniProtKB/TrEMBL
      A6K2V3, A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (3) summary
      PHA03307
      Location:730 → 956
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam01437
      Location:517 → 538
      PSI; Plexin repeat
      cl15693
      Location:52 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    14. XM_006232869.5 → XP_006232931.1  semaphorin-6C isoform X3

      UniProtKB/TrEMBL
      A6K2W3, A6K2W4, Q8R4U4
      Conserved Domains (2) summary
      pfam01437
      Location:472 → 493
      PSI; Plexin repeat
      cl15693
      Location:32 → 471
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9WTL3.1 GenPept UniProtKB/Swiss-Prot:Q9WTL3

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