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    SPG11 SPG11, spatacsin vesicle trafficking associated [ Homo sapiens (human) ]

    Gene ID: 80208, updated on 19-May-2018
    Official Symbol
    SPG11provided by HGNC
    Official Full Name
    SPG11, spatacsin vesicle trafficking associatedprovided by HGNC
    Primary source
    HGNC:HGNC:11226
    See related
    Ensembl:ENSG00000104133 MIM:610844; Vega:OTTHUMG00000131199
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ALS5; CMT2X; KIAA1840
    Summary
    The protein encoded by this gene is a potential transmembrane protein that is phosphorylated upon DNA damage. Defects in this gene are a cause of spastic paraplegia type 11 (SPG11). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]
    Expression
    Ubiquitous expression in thyroid (RPKM 18.4), testis (RPKM 13.2) and 25 other tissues See more
    Orthologs
    See SPG11 in Genome Data Viewer
    Location:
    15q21.1
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 15 NC_000015.10 (44562696..44663678, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (44854894..44955876, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene CTD small phosphatase like 2 Neighboring gene heterogeneous nuclear ribonucleoprotein M pseudogene 1 Neighboring gene EIF3J divergent transcript Neighboring gene eukaryotic translation initiation factor 3 subunit J Neighboring gene PAT1 homolog 2 Neighboring gene beta-2-microglobulin

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ21439, DKFZp762B1512

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    axo-dendritic transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    axon extension IEA
    Inferred from Electronic Annotation
    more info
     
    chemical synaptic transmission IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    phagosome-lysosome fusion involved in apoptotic cell clearance IEA
    Inferred from Electronic Annotation
    more info
     
    synaptic vesicle transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    walking behavior IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    axon IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    lysosomal membrane HDA PubMed 
    nucleolus IDA
    Inferred from Direct Assay
    more info
     
    plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    spatacsin
    Names
    colorectal carcinoma-associated protein
    spastic paraplegia 11 (autosomal recessive)
    spastic paraplegia 11 protein

    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.

    Genomic

    1. NG_008885.1 RefSeqGene

      Range
      5001..105983
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001160227.1NP_001153699.1  spatacsin isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two alternate in-frame exons in the 3' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      BC094704, BC150640, DA926289
      Consensus CDS
      CCDS53939.1
      UniProtKB/Swiss-Prot
      Q96JI7
      Related
      ENSP00000445278.2, OTTHUMP00000247091, ENST00000535302.6, OTTHUMT00000415729
      Conserved Domains (1) summary
      pfam14649
      Location:19822274
      Spatacsin_C; Spatacsin C-terminus
    2. NM_025137.3NP_079413.3  spatacsin isoform 1

      See identical proteins and their annotated locations for NP_079413.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB058743, AC009996, BC094704
      Consensus CDS
      CCDS10112.1
      UniProtKB/Swiss-Prot
      Q96JI7
      Related
      ENSP00000261866.7, OTTHUMP00000161846, ENST00000261866.11, OTTHUMT00000253927
      Conserved Domains (1) summary
      pfam14649
      Location:20952387
      Spatacsin_C; Spatacsin C-terminus

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p12 Primary Assembly

      Range
      44562696..44663678 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006720700.1XP_006720763.1  spatacsin isoform X2

      Conserved Domains (1) summary
      pfam14649
      Location:20472339
      Spatacsin_C; Spatacsin C-terminus
    2. XM_017022634.1XP_016878123.1  spatacsin isoform X1

      Related
      ENSP00000453599.1, OTTHUMP00000247093, ENST00000558319.5, OTTHUMT00000415731
    3. XM_017022636.1XP_016878125.1  spatacsin isoform X5

      Conserved Domains (1) summary
      pfam14649
      Location:10541346
      Spatacsin_C; Spatacsin C-terminus
    4. XM_006720701.3XP_006720764.1  spatacsin isoform X4

    5. XM_017022635.2XP_016878124.1  spatacsin isoform X3

    RNA

    1. XR_931917.2 RNA Sequence

    2. XR_001751402.1 RNA Sequence

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