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    Spg11 SPG11 vesicle trafficking associated, spatacsin [ Rattus norvegicus (Norway rat) ]

    Gene ID: 311372, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Spg11provided by RGD
    Official Full Name
    SPG11 vesicle trafficking associated, spatacsinprovided by RGD
    Primary source
    RGD:1562529
    See related
    EnsemblRapid:ENSRNOG00000021954 AllianceGenome:RGD:1562529
    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
    Also known as
    RGD1562529
    Summary
    Predicted to enable protein kinase binding activity. Predicted to be involved in several processes, including axo-dendritic transport; axonogenesis; and synaptic vesicle transport. Predicted to act upstream of or within several processes, including axonogenesis; cholesterol efflux; and vacuole organization. Located in cytoplasm. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease axonal type 2X; amyotrophic lateral sclerosis type 5; and hereditary spastic paraplegia 11. Orthologous to human SPG11 (SPG11 vesicle trafficking associated, spatacsin). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 156.8), Thymus (RPKM 142.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Spg11 in Genome Data Viewer
    Location:
    3q35
    Exon count:
    40
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (129453118..129526469, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (109007658..109072904, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (113999600..114064438, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene golgi membrane protein 2 Neighboring gene prohibitin 2, pseudogene 2 Neighboring gene CTD small phosphatase like 2 Neighboring gene uncharacterized LOC134486142 Neighboring gene eukaryotic translation initiation factor 3, subunit J Neighboring gene PAT1 homolog 2 Neighboring gene beta-2 microglobulin

    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. Mutations in SPG11, encoding spatacsin, are a major cause of spastic paraplegia with thin corpus callosum. Stevanin G, et al. Nat Genet, 2007 Mar. PMID 17322883
    2. Dysfunction of spatacsin leads to axonal pathology in SPG11-linked hereditary spastic paraplegia. Pérez-Brangulí F, et al. Hum Mol Genet, 2014 Sep 15. PMID 24794856, Free PMC Article
    3. Cellular distribution and subcellular localization of spatacsin and spastizin, two proteins involved in hereditary spastic paraplegia. Murmu RP, et al. Mol Cell Neurosci, 2011 Jul. PMID 21545838
    4. In Vivo Evidence for Lysosome Depletion and Impaired Autophagic Clearance in Hereditary Spastic Paraplegia Type SPG11. Varga RE, et al. PLoS Genet, 2015 Aug. PMID 26284655, Free PMC Article
    5. Integral and associated lysosomal membrane proteins. Schröder B, et al. Traffic, 2007 Dec. PMID 17897319

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within autophagosome organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axo-dendritic transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within axo-dendritic transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axo-dendritic transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within axon extension ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chemical synaptic transmission IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chemical synaptic transmission ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cholesterol efflux ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within corticospinal tract morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within intracellular protein transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within localization within membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within lysosome organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within memory ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within motor behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within motor neuron apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuromuscular junction development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuron apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within phagosome-lysosome fusion involved in apoptotic cell clearance ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein import into nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of store-operated calcium entry ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within skeletal muscle fiber development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in synaptic vesicle transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic vesicle transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in vesicle transport along microtubule IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within vesicle transport along microtubule ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within walking behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in axon ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasmic vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in dendrite ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synapse ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    spatacsin
    Names
    SPG11, spatacsin vesicle trafficking associated
    spastic paraplegia 11 (autosomal recessive)

    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_001415924.1 → NP_001402853.1  spatacsin

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      A0A0G2JZP7, A0A8I6G5Q3
      Related
      ENSRNOP00000071131.3, ENSRNOT00000080253.3

    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
      129453118..129526469 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017591740.3 → XP_017447229.1  spatacsin isoform X1

      UniProtKB/TrEMBL
      A0A8I6G5Q3

    2. XM_039104972.2 → XP_038960900.1  spatacsin isoform X2

      UniProtKB/TrEMBL
      A6HPR4
      Conserved Domains (1) summary
      pfam14649
      Location:1229 → 1521
      Spatacsin_C; Spatacsin C-terminus

    3. XM_039104973.2 → XP_038960901.1  spatacsin isoform X3

      UniProtKB/TrEMBL
      A6HPR4
      Conserved Domains (1) summary
      pfam14649
      Location:1021 → 1313
      Spatacsin_C; Spatacsin C-terminus

    RNA

    1. XR_005501873.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001191571.1: Suppressed sequence

      Description
      NM_001191571.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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