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

Gene ID: 80208, updated on 19-Nov-2022

Summary

Official Symbol
SPG11provided by HGNC
Official Full Name
SPG11 vesicle trafficking associated, spatacsinprovided by HGNC
Primary source
HGNC:HGNC:11226
See related
Ensembl:ENSG00000104133 MIM:610844; AllianceGenome:HGNC:11226
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
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Genomic context

See SPG11 in Genome Data Viewer
Location:
15q21.1
Exon count:
42
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (44562696..44663662, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (42370662..42471634, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (44854894..44955860, 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 microRNA 10393 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What'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
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein kinase binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within autophagosome organization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in axo-dendritic transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in axo-dendritic transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in axon extension IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in chemical synaptic transmission IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cholesterol efflux IEA
Inferred from Electronic Annotation
more info
 
involved_in corticospinal tract morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in localization within membrane IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within lysosome organization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in memory IEA
Inferred from Electronic Annotation
more info
 
involved_in motor behavior IEA
Inferred from Electronic Annotation
more info
 
involved_in motor neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in neuromuscular junction development IEA
Inferred from Electronic Annotation
more info
 
involved_in phagosome-lysosome fusion involved in apoptotic cell clearance IEA
Inferred from Electronic Annotation
more info
 
involved_in protein import into nucleus IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of store-operated calcium entry IEA
Inferred from Electronic Annotation
more info
 
involved_in skeletal muscle fiber development IEA
Inferred from Electronic Annotation
more info
 
involved_in synaptic vesicle transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in synaptic vesicle transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in walking behavior IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in dendrite IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in lysosomal membrane HDA PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 
is_active_in synapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in synapse IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
spatacsin
Names
SPG11, spatacsin vesicle trafficking associated
amyotrophic lateral sclerosis 5
colorectal carcinoma-associated protein
spastic paraplegia 11 (autosomal recessive)
spastic paraplegia 11 protein

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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
    5017..105983
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001160227.2NP_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
    Consensus CDS
    CCDS53939.1
    UniProtKB/Swiss-Prot
    Q96JI7
    Related
    ENSP00000445278.2, ENST00000535302.6
    Conserved Domains (1) summary
    pfam14649
    Location:19822274
    Spatacsin_C; Spatacsin C-terminus
  2. NM_001411132.1NP_001398061.1  spatacsin isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC009996
    Consensus CDS
    CCDS91991.1
    UniProtKB/TrEMBL
    A0A804HID9
  3. NM_025137.4NP_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, Q9H734
    Related
    ENSP00000261866.7, ENST00000261866.12
    Conserved Domains (1) summary
    pfam14649
    Location:20952387
    Spatacsin_C; Spatacsin C-terminus

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    44562696..44663662 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006720700.2XP_006720763.1  spatacsin isoform X1

    Related
    ENSP00000507025.1, ENST00000682065.1
    Conserved Domains (1) summary
    pfam14649
    Location:20472339
    Spatacsin_C; Spatacsin C-terminus
  2. XM_047433144.1XP_047289100.1  spatacsin isoform X2

  3. XM_047433146.1XP_047289102.1  spatacsin isoform X6

  4. XM_006720701.4XP_006720764.1  spatacsin isoform X4

    Related
    ENSP00000508089.1, ENST00000682788.1
  5. XM_017022635.3XP_016878124.1  spatacsin isoform X3

  6. XM_047433145.1XP_047289101.1  spatacsin isoform X5

    Related
    ENSP00000507557.1, ENST00000683121.1

RNA

  1. XR_001751402.2 RNA Sequence

    Related
    ENST00000682915.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    42370662..42471634 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)