U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    Sema6d semaphorin 6D [ Rattus norvegicus (Norway rat) ]

    Gene ID: 311384, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Sema6dprovided by RGD
    Official Full Name
    semaphorin 6Dprovided by RGD
    Primary source
    RGD:1310910
    See related
    EnsemblRapid:ENSRNOG00000004812 AllianceGenome:RGD:1310910
    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; neuropilin binding activity; and semaphorin receptor binding activity. Predicted to be involved in several processes, including negative regulation of axon extension; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to act upstream of or within negative regulation of smooth muscle cell migration; positive regulation of smooth muscle cell migration; and ventricular system development. Predicted to be located in Golgi apparatus and cell surface. Predicted to be active in plasma membrane. Orthologous to human SEMA6D (semaphorin 6D). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Lung (RPKM 79.6), Brain (RPKM 63.1) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Sema6d in Genome Data Viewer
    Location:
    3q36
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (131801680..132394578)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (111883415..111941100)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (116899906..116958059)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA48 Neighboring gene adenosylhomocysteinase, pseudogene 8 Neighboring gene uncharacterized LOC134486432 Neighboring gene uncharacterized LOC120101648 Neighboring gene uncharacterized LOC102555070 Neighboring gene uncharacterized LOC134486433 Neighboring gene uncharacterized LOC108350455

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. SEMA6D, Negatively Regulated by miR-7, Contributes to C28/I2 chondrocyte's Catabolic and Anabolic Activities via p38 Signaling Pathway. Yang H, et al. Oxid Med Cell Longev, 2022. PMID 35757507, Free PMC Article
    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. Stromal expression of decorin, Semaphorin6D, SPARC, Sprouty1 and Tsukushi in developing prostate and decreased levels of decorin in prostate cancer. Henke A, et al. PLoS One, 2012. PMID 22880013, Free PMC Article
    4. Dual roles of Sema6D in cardiac morphogenesis through region-specific association of its receptor, Plexin-A1, with off-track and vascular endothelial growth factor receptor type 2. Toyofuku T, et al. Genes Dev, 2004 Feb 15. PMID 14977921, Free PMC Article
    5. 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

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SEMA6D, Negatively Regulated by miR-7, Contributes to C28/I2 chondrocyte's Catabolic and Anabolic Activities via p38 Signaling Pathway.
      Title: SEMA6D, Negatively Regulated by miR-7, Contributes to C28/I2 chondrocyte's Catabolic and Anabolic Activities via p38 Signaling Pathway.
    2. The spatio-temporal expression of Decorin, Semaphorin6D, SPARC, Spry-1 and Tsukushi in developing prostate is described and observed similar mesenchymal expression patterns in rat and human.
      Title: Stromal expression of decorin, Semaphorin6D, SPARC, Sprouty1 and Tsukushi in developing prostate and decreased levels of decorin in prostate cancer.
    Submit: New GeneRIF Correction

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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
    		  
    enables semaphorin receptor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 negative regulation of axon extension ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of smooth muscle cell migration 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
    		  
    acts_upstream_of_or_within positive regulation of smooth muscle cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of smooth muscle cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within ventricular system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    semaphorin-6D
    Names
    sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001107768.1 → NP_001101238.1  semaphorin-6D precursor

      See identical proteins and their annotated locations for NP_001101238.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473949
      UniProtKB/TrEMBL
      A0A8I5ZWU1, A6HPV2, D3ZDA2
      Related
      ENSRNOP00000062577.1, ENSRNOT00000066101.3
      Conserved Domains (2) summary
      pfam01437
      Location:493 → 561
      PSI; Plexin repeat
      cl15693
      Location:49 → 492
      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_086021.1 Reference GRCr8

      Range
      131801680..132394578
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063283741.1 → XP_063139811.1  semaphorin-6D isoform X6

    2. XM_039104985.2 → XP_038960913.1  semaphorin-6D isoform X6

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Conserved Domains (2) summary
      pfam01437
      Location:514 → 543
      PSI; Plexin repeat
      cl15693
      Location:49 → 513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    3. XM_039104984.2 → XP_038960912.1  semaphorin-6D isoform X6

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Conserved Domains (2) summary
      pfam01437
      Location:514 → 543
      PSI; Plexin repeat
      cl15693
      Location:49 → 513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    4. XM_063283739.1 → XP_063139809.1  semaphorin-6D isoform X1

    5. XM_039104982.2 → XP_038960910.2  semaphorin-6D isoform X2

    6. XM_063283743.1 → XP_063139813.1  semaphorin-6D isoform X8

    7. XM_017591743.3 → XP_017447232.2  semaphorin-6D isoform X10

      UniProtKB/TrEMBL
      A0A8I5ZWU1, A0A8I6AKL1
      Related
      ENSRNOP00000094338.1, ENSRNOT00000102426.2
      Conserved Domains (2) summary
      pfam01437
      Location:514 → 543
      PSI; Plexin repeat
      cl15693
      Location:49 → 513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    8. XM_039104983.2 → XP_038960911.1  semaphorin-6D isoform X5

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Conserved Domains (2) summary
      pfam01437
      Location:514 → 543
      PSI; Plexin repeat
      cl15693
      Location:49 → 513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    9. XM_063283742.1 → XP_063139812.1  semaphorin-6D isoform X7

    10. XM_017591744.3 → XP_017447233.2  semaphorin-6D isoform X12

      UniProtKB/TrEMBL
      A0A8I5ZVU9, A0A8I5ZWU1
      Related
      ENSRNOP00000082908.1, ENSRNOT00000098848.2
      Conserved Domains (2) summary
      pfam01437
      Location:514 → 543
      PSI; Plexin repeat
      cl15693
      Location:49 → 513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    11. XM_008762171.4 → XP_008760393.2  semaphorin-6D isoform X3

      UniProtKB/TrEMBL
      A0A0G2JZC4, A0A8I6GKS5
      Conserved Domains (2) summary
      pfam01437
      Location:514 → 569
      PSI; Plexin repeat
      cl15693
      Location:49 → 513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    12. XM_008762172.4 → XP_008760394.2  semaphorin-6D isoform X4

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Related
      ENSRNOP00000070994.3, ENSRNOT00000090802.3
      Conserved Domains (2) summary
      pfam01437
      Location:514 → 569
      PSI; Plexin repeat
      cl15693
      Location:49 → 513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    13. XM_008762174.4 → XP_008760396.2  semaphorin-6D isoform X11

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Conserved Domains (2) summary
      pfam01437
      Location:514 → 569
      PSI; Plexin repeat
      cl15693
      Location:49 → 513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    14. XM_063283744.1 → XP_063139814.1  semaphorin-6D isoform X9

      Related
      ENSRNOP00000093722.2, ENSRNOT00000109949.2

    15. XM_008762175.4 → XP_008760397.2  semaphorin-6D isoform X13

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Conserved Domains (2) summary
      pfam01437
      Location:514 → 569
      PSI; Plexin repeat
      cl15693
      Location:49 → 513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    16. XM_063283745.1 → XP_063139815.1  semaphorin-6D isoform X14

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools