U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 311384, updated on 11-Apr-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
Ensembl: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 and semaphorin receptor binding activity. Predicted to be involved in several processes, including generation of neurons; 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; cell surface; and plasma membrane. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Orthologous to human SEMA6D (semaphorin 6D). [provided by Alliance of Genome Resources, Apr 2022]
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
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
  • 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 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 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, ENSRNOT00000066101.2
    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
    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
    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
    Related
    ENSRNOP00000070994.2
    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
    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

  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
Miscellaneous