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    Sema6a semaphorin 6A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361324, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Sema6aprovided by RGD
    Official Full Name
    semaphorin 6Aprovided by RGD
    Primary source
    RGD:1305493
    See related
    EnsemblRapid:ENSRNOG00000004033 AllianceGenome:RGD:1305493
    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 identical protein binding activity; signaling receptor binding activity; and transmembrane signaling receptor activity. Predicted to be involved in several processes, including generation of neurons; negative regulation of cell adhesion involved in sprouting angiogenesis; and negative regulation of signal transduction. Predicted to act upstream of or within cell surface receptor signaling pathway and centrosome localization. Predicted to be active in plasma membrane. Orthologous to human SEMA6A (semaphorin 6A). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 118.1), Kidney (RPKM 79.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sema6a in Genome Data Viewer
    Location:
    18q11
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 18 NC_086036.1 (42237227..42358540, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 18 NC_051353.1 (40050623..40171954, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (41330519..41451813, complement)

    Chromosome 18 - NC_086036.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134482946 Neighboring gene uncharacterized LOC134482943 Neighboring gene uncharacterized LOC134482944 Neighboring gene uncharacterized LOC134482945 Neighboring gene cytochrome c oxidase subunit 6C-2-like Neighboring gene uncharacterized LOC134482947 Neighboring gene small nucleolar RNA SNORA48

    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. Semaphorin 6A improves functional recovery in conjunction with motor training after cerebral ischemia. Rogalewski A, et al. PLoS One, 2010 May 20. PMID 20505770, Free PMC Article
    2. The transmembrane semaphorin Sema6A controls cerebellar granule cell migration. Kerjan G, et al. Nat Neurosci, 2005 Nov. PMID 16205717
    3. Structural basis for semaphorin signalling through the plexin receptor. Nogi T, et al. Nature, 2010 Oct 28. PMID 20881961
    4. Plexin-A2 and its ligand, Sema6A, control nucleus-centrosome coupling in migrating granule cells. Renaud J, et al. Nat Neurosci, 2008 Apr. PMID 18327254
    5. MicroRNA-27a/b controls endothelial cell repulsion and angiogenesis by targeting semaphorin 6A. Urbich C, et al. Blood, 2012 Feb 9. PMID 22184411

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Semaphorin 6a overexpressed in the cortex enhances recovery after cerebral ischemia.
      Title: Semaphorin 6A improves functional recovery in conjunction with motor training after cerebral ischemia.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    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 identical protein binding ISO
    Inferred from Sequence Orthology
    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
    		  
    enables transmembrane signaling receptor activity 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cell surface receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to vascular endothelial growth factor stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within centrosome localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of ERK1 and ERK2 cascade ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of angiogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of cell adhesion involved in sprouting angiogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of sprouting angiogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of vascular endothelial growth factor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neuron migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of neuron migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of neuron migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in semaphorin-plexin signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    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

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    Preferred Names
    semaphorin-6A
    Names
    sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A
    semaphorin 6A-1

    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_001108430.3 → NP_001101900.2  semaphorin-6A isoform 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      JAXUCZ010000018
      UniProtKB/TrEMBL
      A6IWY3, D3ZAG0
      Related
      ENSRNOP00000005476.7, ENSRNOT00000005476.10
      Conserved Domains (2) summary
      cd11266
      Location:48 → 513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514 → 544
      PSI; Plexin repeat

    2. NM_001372354.2 → NP_001359283.1  semaphorin-6A isoform 2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      JAXUCZ010000018
      UniProtKB/TrEMBL
      A0A8I5ZYF8
      Related
      ENSRNOP00000099981.1, ENSRNOT00000150263.1
      Conserved Domains (2) summary
      cd11266
      Location:48 → 513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514 → 546
      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_086036.1 Reference GRCr8

      Range
      42237227..42358540 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063277473.1 → XP_063133543.1  semaphorin-6A isoform X3

      Related
      ENSRNOP00000082708.2, ENSRNOT00000115179.2

    2. XM_039096967.2 → XP_038952895.1  semaphorin-6A isoform X1

      UniProtKB/TrEMBL
      D3ZAX7
      Conserved Domains (2) summary
      cd11266
      Location:48 → 513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514 → 544
      PSI; Plexin repeat

    3. XM_003751782.6 → XP_003751830.1  semaphorin-6A isoform X1

      See identical proteins and their annotated locations for XP_003751830.1

      UniProtKB/TrEMBL
      D3ZAX7
      Related
      ENSRNOP00000005446.5, ENSRNOT00000005446.7
      Conserved Domains (2) summary
      cd11266
      Location:48 → 513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514 → 544
      PSI; Plexin repeat

    4. XM_063277472.1 → XP_063133542.1  semaphorin-6A isoform X2

      UniProtKB/TrEMBL
      A6IWY3, D3ZAG0
    Nucleotide Protein Strain
    Heading Accession and Version

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