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

    Gene ID: 311384, updated on 9-Dec-2024

    Summary

    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, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 79.6), Brain (RPKM 63.1) and 9 other tissues See more
    Orthologs
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    Genomic context

    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

    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

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chemorepellent activity  
    enables receptor ligand activity  
    enables semaphorin receptor binding  
    enables semaphorin receptor binding  
    Component Evidence Code Pubs
    located_in Golgi apparatus  
    located_in Golgi apparatus  
    located_in cell surface  
    located_in cytoplasm  
    is_active_in plasma membrane  
    located_in plasma membrane  

    General protein information

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

    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_001107768.1NP_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:493561
      PSI; Plexin repeat
      cl15693
      Location:49492
      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_063283741.1XP_063139811.1  semaphorin-6D isoform X6

      UniProtKB/TrEMBL
      A0A8I6GKS5
    2. XM_039104985.2XP_038960913.1  semaphorin-6D isoform X6

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Conserved Domains (2) summary
      pfam01437
      Location:514543
      PSI; Plexin repeat
      cl15693
      Location:49513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    3. XM_039104984.2XP_038960912.1  semaphorin-6D isoform X6

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Conserved Domains (2) summary
      pfam01437
      Location:514543
      PSI; Plexin repeat
      cl15693
      Location:49513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    4. XM_063283739.1XP_063139809.1  semaphorin-6D isoform X1

      UniProtKB/TrEMBL
      A0A8I6GKS5
    5. XM_039104982.2XP_038960910.2  semaphorin-6D isoform X2

      UniProtKB/TrEMBL
      A0A8I6GKS5
    6. XM_063283743.1XP_063139813.1  semaphorin-6D isoform X8

      UniProtKB/TrEMBL
      A0A8I6GKS5
    7. XM_017591743.3XP_017447232.2  semaphorin-6D isoform X10

      UniProtKB/TrEMBL
      A0A8I5ZWU1, A0A8I6AKL1
      Related
      ENSRNOP00000094338.1, ENSRNOT00000102426.2
      Conserved Domains (2) summary
      pfam01437
      Location:514543
      PSI; Plexin repeat
      cl15693
      Location:49513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    8. XM_039104983.2XP_038960911.1  semaphorin-6D isoform X5

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Conserved Domains (2) summary
      pfam01437
      Location:514543
      PSI; Plexin repeat
      cl15693
      Location:49513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    9. XM_063283742.1XP_063139812.1  semaphorin-6D isoform X7

      UniProtKB/TrEMBL
      A0A8I6GKS5
    10. XM_017591744.3XP_017447233.2  semaphorin-6D isoform X12

      UniProtKB/TrEMBL
      A0A8I5ZVU9, A0A8I5ZWU1
      Related
      ENSRNOP00000082908.1, ENSRNOT00000098848.2
      Conserved Domains (2) summary
      pfam01437
      Location:514543
      PSI; Plexin repeat
      cl15693
      Location:49513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    11. XM_008762171.4XP_008760393.2  semaphorin-6D isoform X3

      UniProtKB/TrEMBL
      A0A0G2JZC4, A0A8I6GKS5
      Conserved Domains (2) summary
      pfam01437
      Location:514569
      PSI; Plexin repeat
      cl15693
      Location:49513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    12. XM_008762172.4XP_008760394.2  semaphorin-6D isoform X4

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Related
      ENSRNOP00000070994.3, ENSRNOT00000090802.3
      Conserved Domains (2) summary
      pfam01437
      Location:514569
      PSI; Plexin repeat
      cl15693
      Location:49513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    13. XM_008762174.4XP_008760396.2  semaphorin-6D isoform X11

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Conserved Domains (2) summary
      pfam01437
      Location:514569
      PSI; Plexin repeat
      cl15693
      Location:49513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    14. XM_063283744.1XP_063139814.1  semaphorin-6D isoform X9

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Related
      ENSRNOP00000093722.2, ENSRNOT00000109949.2
    15. XM_008762175.4XP_008760397.2  semaphorin-6D isoform X13

      UniProtKB/TrEMBL
      A0A8I6GKS5
      Conserved Domains (2) summary
      pfam01437
      Location:514569
      PSI; Plexin repeat
      cl15693
      Location:49513
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    16. XM_063283745.1XP_063139815.1  semaphorin-6D isoform X14

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