U.S. flag

An official website of the United States government

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

Gene ID: 80208, updated on 10-Dec-2024

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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See SPG11 in Genome Data Viewer
Location:
15q21.1
Exon count:
42
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (44562696..44663662, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (42370662..42471634, complement)
RS_2024_09 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 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:44828013-44828800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6397 Neighboring gene EIF3J divergent transcript Neighboring gene eukaryotic translation initiation factor 3 subunit J Neighboring gene ReSE screen-validated silencer GRCh37_chr15:44874604-44874775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6398 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:44879793-44880004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9341 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:44936676-44936780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9342 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:44955204-44956160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9347 Neighboring gene PAT1 homolog 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:45003536-45004198 Neighboring gene microRNA 10393 Neighboring gene beta-2-microglobulin

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Amyotrophic lateral sclerosis type 5 not available
Charcot-Marie-Tooth disease axonal type 2X
MedGen: C5569024 OMIM: 616668 GeneReviews: Not available
not available
Hereditary spastic paraplegia 11
MedGen: C1858479 OMIM: 604360 GeneReviews: Spastic Paraplegia 11
not available

Interactions

General gene information

Clone Names

  • FLJ21439, DKFZp762B1512

Gene Ontology Provided by GOA

Process Evidence Code Pubs
acts_upstream_of_or_within autophagosome organization PubMed 
involved_in axo-dendritic transport  
involved_in axo-dendritic transport PubMed 
involved_in axon extension  
involved_in axonogenesis  
involved_in chemical synaptic transmission  
involved_in chemical synaptic transmission PubMed 
involved_in cholesterol efflux  
involved_in corticospinal tract morphogenesis  
involved_in localization within membrane  
acts_upstream_of_or_within lysosome organization PubMed 
involved_in memory  
involved_in motor behavior  
involved_in motor neuron apoptotic process  
involved_in neuromuscular junction development  
involved_in phagosome-lysosome fusion involved in apoptotic cell clearance  
involved_in protein catabolic process  
involved_in protein import into nucleus  
involved_in regulation of store-operated calcium entry  
involved_in skeletal muscle fiber development  
involved_in synaptic vesicle transport  
involved_in synaptic vesicle transport PubMed 
involved_in vesicle transport along microtubule  
involved_in walking behavior  
Component Evidence Code Pubs
is_active_in axon  
is_active_in cytoplasm  
located_in cytoplasm PubMed 
located_in cytoplasmic vesicle PubMed 
located_in cytosol  
located_in cytosol  
is_active_in dendrite  
located_in endoplasmic reticulum  
located_in lysosomal membrane PubMed 
located_in nucleolus  
located_in plasma membrane  
is_active_in synapse  
located_in synapse 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/TrEMBL
    H0YLK7
    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, C4B7M4
    Related
    ENSP00000507025.1, ENST00000682065.1
  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
    A8KAX9, B9EK60, F5H3N6, Q4VC11, Q58G86, Q69YG6, Q6NW01, Q8N270, Q8TBU9, Q96JI7, Q9H734
    UniProtKB/TrEMBL
    C4B7M4
    Related
    ENSP00000261866.7, ENST00000261866.12
    Conserved Domains (1) summary
    pfam14649
    Location:20952387
    Spatacsin_C; Spatacsin C-terminus

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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_047433144.1XP_047289100.1  spatacsin isoform X1

    UniProtKB/TrEMBL
    C4B7M4
  2. XM_047433146.1XP_047289102.1  spatacsin isoform X5

  3. XM_006720701.4XP_006720764.1  spatacsin isoform X3

    UniProtKB/TrEMBL
    A0A804HKV6
    Related
    ENSP00000508089.1, ENST00000682788.1
  4. XM_017022635.3XP_016878124.1  spatacsin isoform X2

    UniProtKB/TrEMBL
    A0A804HKV6
  5. XM_047433145.1XP_047289101.1  spatacsin isoform X4

    UniProtKB/TrEMBL
    A0A804HJL9
    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)

mRNA and Protein(s)

  1. XM_054378921.1XP_054234896.1  spatacsin isoform X1

    UniProtKB/TrEMBL
    C4B7M4
  2. XM_054378925.1XP_054234900.1  spatacsin isoform X5

  3. XM_054378923.1XP_054234898.1  spatacsin isoform X3

    UniProtKB/TrEMBL
    A0A804HKV6
  4. XM_054378922.1XP_054234897.1  spatacsin isoform X2

    UniProtKB/TrEMBL
    A0A804HKV6
  5. XM_054378924.1XP_054234899.1  spatacsin isoform X4

    UniProtKB/TrEMBL
    A0A804HJL9

RNA

  1. XR_008489013.1 RNA Sequence

External link. Please review our privacy policy.