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    Sema5a semaphorin 5A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 310207, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Sema5aprovided by RGD
    Official Full Name
    semaphorin 5Aprovided by RGD
    Primary source
    RGD:1308650
    See related
    Ensembl:ENSRNOG00000011977 AllianceGenome:RGD:1308650
    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
    Enables chondroitin sulfate proteoglycan binding activity; heparan sulfate proteoglycan binding activity; and syndecan binding activity. Involved in nervous system development and signal clustering. Located in membrane. Orthologous to human SEMA5A (semaphorin 5A). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Kidney (RPKM 139.5), Uterus (RPKM 136.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    2q23
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (85020724..85451938)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (83309843..83741084)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (85377318..85808970)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene succinate dehydrogenase complex assembly factor 4, pseudogene 1 Neighboring gene uncharacterized LOC100909539 Neighboring gene uncharacterized LOC134485782 Neighboring gene small nucleolar RNA, C/D box 123 Neighboring gene U6 spliceosomal RNA Neighboring gene uncharacterized LOC134485871

    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. Semaphorin5A expression in the developing chick telencephalon. Pineda D, et al. Brain Res Bull, 2005 Sep 15. PMID 16144627
    2. Semaphorin 5A is a bifunctional axon guidance cue regulated by heparan and chondroitin sulfate proteoglycans. Kantor DB, et al. Neuron, 2004 Dec 16. PMID 15603739
    3. Molecular cloning and mapping of human semaphorin F from the Cri-du-chat candidate interval. Simmons AD, et al. Biochem Biophys Res Commun, 1998 Jan 26. PMID 9464278
    4. Semaphorin 5A promotes angiogenesis by increasing endothelial cell proliferation, migration, and decreasing apoptosis. Sadanandam A, et al. Microvasc Res, 2010 Jan. PMID 19850054, Free PMC Article
    5. Invariant Sema5A inhibition serves an ensheathing function during optic nerve development. Oster SF, et al. Development, 2003 Feb. PMID 12506007

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Semaphorin5A expression in the developing chick telencephalon.
      Title: Semaphorin5A expression in the developing chick telencephalon.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables axon guidance receptor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chondroitin sulfate proteoglycan binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables heparan sulfate proteoglycan binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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
    		  
    enables semaphorin receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables syndecan binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in axon extension IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within axon extension ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within axon guidance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axonal fasciculation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in blood vessel endothelial cell proliferation involved in sprouting angiogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in blood vessel endothelial cell proliferation involved in sprouting angiogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within branching involved in blood vessel morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within branching morphogenesis of an epithelial tube ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell chemotaxis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell chemotaxis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within detection of light stimulus involved in visual perception ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in diencephalon development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative chemotaxis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of axon extension involved in axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of cell adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of cell adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of endothelial cell apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of endothelial cell apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within neuron projection extension ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuron projection guidance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive chemotaxis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive chemotaxis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of actin filament depolymerization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of actin filament depolymerization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of angiogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of angiogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of axon extension involved in axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of canonical Wnt signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of endothelial cell chemotaxis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of endothelial cell chemotaxis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of endothelial cell proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of endothelial cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    involved_in semaphorin-plexin signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in signal clustering IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in signal clustering ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in signal clustering ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    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-5A
    Names
    sema F
    sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A
    semaphorin-F

    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_001107659.2 → NP_001101129.1  semaphorin-5A precursor

      See identical proteins and their annotated locations for NP_001101129.1

      Status: VALIDATED

      Source sequence(s)
      AABR07009051, AABR07009052
      UniProtKB/Swiss-Prot
      D3ZTD8
      Related
      ENSRNOP00000016506.4, ENSRNOT00000016506.6
      Conserved Domains (3) summary
      cd11263
      Location:50 → 485
      Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)
      smart00209
      Location:598 → 651
      TSP1; Thrombospondin type 1 repeats
      pfam01437
      Location:486 → 533
      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_086020.1 Reference GRCr8

      Range
      85020724..85451938
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063281754.1 → XP_063137824.1  semaphorin-5A isoform X1

      UniProtKB/Swiss-Prot
      D3ZTD8

    2. XM_063281755.1 → XP_063137825.1  semaphorin-5A isoform X1

      UniProtKB/Swiss-Prot
      D3ZTD8
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    D3ZTD8.1 GenPept UniProtKB/Swiss-Prot:D3ZTD8

    Gene LinkOut

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

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