Spg11 SPG11, spatacsin vesicle trafficking associated [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Spg11provided by MGI
Official Full Name: SPG11, spatacsin vesicle trafficking associatedprovided by MGI
Primary source: MGI:MGI:2444989
See related: Ensembl:ENSMUSG00000033396 AllianceGenome:MGI:2444989
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: A330015I11; 6030465E24Rik; C530005A01Rik
Summary: Acts upstream of or within several processes, including axonogenesis; cholesterol efflux; and motor neuron apoptotic process. Located in several cellular components, including axon; cytosol; and dendrite. Used to study hereditary spastic paraplegia 11. 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, Apr 2022]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 7.0), limb E14.5 (RPKM 6.7) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 E5; 2 60.5 cM

Exon count:: 41

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (121884001..121949915, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (122053526..122119434, complement)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Spatacsin regulates directionality of lysosome trafficking by promoting the degradation of its partner AP5Z1.
Title: Spatacsin regulates directionality of lysosome trafficking by promoting the degradation of its partner AP5Z1.
Spg11 knockout mice developed early-onset motor impairment and cognitive deficits. These behavioral deficits were associated with progressive brain atrophy with the loss of neurons in the brain, as well as with accumulation of dystrophic axons in the corticospinal tract. Spinal motor neurons also degenerated and this was accompanied by fragmentation of neuromuscular junctions and muscle atrophy.
Title: Loss of spatacsin function alters lysosomal lipid clearance leading to upper and lower motor neuron degeneration.
Study provides evidence that SPG11 is implicated in axonal maintenance and cargo trafficking.
Title: Dysfunction of spatacsin leads to axonal pathology in SPG11-linked hereditary spastic paraplegia.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (1) 1 citation
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G36404 (e-PCR)
- UniSTS:42770

RH126537 (e-PCR)
- UniSTS:207391

RH126395 (e-PCR)
- UniSTS:163103

RH124823 (e-PCR)
- UniSTS:161645

RH124861 (e-PCR)
- UniSTS:161683

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein kinase binding	ISO Inferred from Sequence Orthology more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within autophagosome organization	ISO Inferred from Sequence Orthology more info	PubMed
involved_in axo-dendritic transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within axo-dendritic transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axo-dendritic transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within axon extension	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axonogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within axonogenesis	ISO Inferred from Sequence Orthology 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	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within corticospinal tract morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within localization within membrane	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lysosome organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lysosome organization	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within memory	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within motor behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within motor neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuromuscular junction development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within phagosome-lysosome fusion involved in apoptotic cell clearance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein import into nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of store-operated calcium entry	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of synaptic plasticity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal muscle fiber development	IMP Inferred from Mutant Phenotype more info	PubMed
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
acts_upstream_of_or_within walking behavior	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic vesicle	ISO Inferred from Sequence Orthology more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleus	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	IMP Inferred from Mutant Phenotype more info	PubMed
located_in synapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: spatacsin

Names: spastic paraplegia 11 protein homolog

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)

NM_145531.3 → NP_663506.2 spatacsin

See identical proteins and their annotated locations for NP_663506.2

Status: VALIDATED

Source sequence(s)

AL845457

Consensus CDS

CCDS50687.1

UniProtKB/Swiss-Prot

A2ARM0, Q3UHA3, Q6ZPH3, Q8BHQ1, Q8C7R3, Q8C7U2, Q8CA88, Q8VEA5

Related

ENSMUSP00000037543.8, ENSMUST00000036450.8

Conserved Domains (1) summary

pfam14649
Location:2082 → 2374

Spatacsin_C; Spatacsin C-terminus

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

121884001..121949915 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011239422.3 → XP_011237724.1 spatacsin isoform X1

Conserved Domains (1) summary

pfam14649
Location:2082 → 2183

Spatacsin_C; Spatacsin C-terminus
XM_011239423.4 → XP_011237725.1 spatacsin isoform X2

RNA

XR_003951843.2 RNA Sequence
XR_004939461.1 RNA Sequence
XR_374438.5 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_172533.1: Suppressed sequence

Description

NM_172533.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.