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

Gene ID: 80208, updated on 5-Aug-2018

Summary

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

Genomic context

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

Genomic regions, transcripts, and products

Expression

  • 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

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 

General protein information

Preferred Names
spatacsin
Names
colorectal carcinoma-associated protein
spastic paraplegia 11 (autosomal recessive)
spastic paraplegia 11 protein

NCBI Reference Sequences (RefSeq)

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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