Version 5.4
Homo sapiens Gene: SMN1
Summary
InnateDB Gene IDBG-26826.6
Last Modified 2014-10-13 [Report errors or provide feedback]
Gene Symbol SMN1
Gene Name survival of motor neuron 1, telomeric
Synonyms BCD541; C-BCD541; GEMIN1; SMA; SMA@; SMA1; SMA2; SMA3; SMA4; SMN; SMNC; SMNT; T-BCD541; TDRD16A; TDRD16B
Species Homo sapiens
Ensembl Gene ENSG00000172062
Encoded Proteins
IDBP-26828
survival of motor neuron 1, telomeric
IDBP-26832
survival of motor neuron 1, telomeric
IDBP-481857
survival of motor neuron 1, telomeric
IDBP-478145
survival of motor neuron 1, telomeric
IDBP-475777
survival of motor neuron 1, telomeric
IDBP-484542
survival of motor neuron 1, telomeric
IDBP-478006
survival of motor neuron 1, telomeric
Protein Structure
Useful resources Stemformatics EHFPI ImmGen
Entrez Gene
Summary This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and complexity of the sequence have also caused difficulty in determining the organization of this genomic region. The telomeric and centromeric copies of this gene are nearly identical and encode the same protein. While mutations in the telomeric copy are associated with spinal muscular atrophy, mutations in this gene, the centromeric copy, do not lead to disease. This gene may be a modifier of disease caused by mutation in the telomeric copy. The critical sequence difference between the two genes is a single nucleotide in exon 7, which is thought to be an exon splice enhancer. Note that the nine exons of both the telomeric and centromeric copies are designated historically as exon 1, 2a, 2b, and 3-8. It is thought that gene conversion events may involve the two genes, leading to varying copy numbers of each gene. The full length protein encoded by this gene localizes to both the cytoplasm and the nucleus. Within the nucleus, the protein localizes to subnuclear bodies called gems which are found near coiled bodies containing high concentrations of small ribonucleoproteins (snRNPs). This protein forms heteromeric complexes with proteins such as SIP1 and GEMIN4, and also interacts with several proteins known to be involved in the biogenesis of snRNPs, such as hnRNP U protein and the small nucleolar RNA binding protein. Four transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Sep 2008] This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and complexity of the sequence have also caused difficulty in determining the organization of this genomic region. The telomeric and centromeric copies of this gene are nearly identical and encode the same protein. However, mutations in this gene, the telomeric copy, are associated with spinal muscular atrophy; mutations in the centromeric copy do not lead to disease. The centromeric copy may be a modifier of disease caused by mutation in the telomeric copy. The critical sequence difference between the two genes is a single nucleotide in exon 7, which is thought to be an exon splice enhancer. Note that the nine exons of both the telomeric and centromeric copies are designated historically as exon 1, 2a, 2b, and 3-8. It is thought that gene conversion events may involve the two genes, leading to varying copy numbers of each gene. The protein encoded by this gene localizes to both the cytoplasm and the nucleus. Within the nucleus, the protein localizes to subnuclear bodies called gems which are found near coiled bodies containing high concentrations of small ribonucleoproteins (snRNPs). This protein forms heteromeric complexes with proteins such as SIP1 and GEMIN4, and also interacts with several proteins known to be involved in the biogenesis of snRNPs, such as hnRNP U protein and the small nucleolar RNA binding protein. Two transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Sep 2008]
This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and complexity of the sequence have also caused difficulty in determining the organization of this genomic region. The telomeric and centromeric copies of this gene are nearly identical and encode the same protein. However, mutations in this gene, the telomeric copy, are associated with spinal muscular atrophy; mutations in the centromeric copy do not lead to disease. The centromeric copy may be a modifier of disease caused by mutation in the telomeric copy. The critical sequence difference between the two genes is a single nucleotide in exon 7, which is thought to be an exon splice enhancer. Note that the nine exons of both the telomeric and centromeric copies are designated historically as exon 1, 2a, 2b, and 3-8. It is thought that gene conversion events may involve the two genes, leading to varying copy numbers of each gene. The protein encoded by this gene localizes to both the cytoplasm and the nucleus. Within the nucleus, the protein localizes to subnuclear bodies called gems which are found near coiled bodies containing high concentrations of small ribonucleoproteins (snRNPs). This protein forms heteromeric complexes with proteins such as SIP1 and GEMIN4, and also interacts with several proteins known to be involved in the biogenesis of snRNPs, such as hnRNP U protein and the small nucleolar RNA binding protein. Multiple transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2014]
Gene Information
Type Protein coding
Genomic Location Chromosome 5:70925030-70953942
Strand Forward strand
Band q13.2
Transcripts
ENST00000380707 ENSP00000370083
ENST00000351205 ENSP00000305857
ENST00000503079 ENSP00000428128
ENST00000514951 ENSP00000423298
ENST00000506239 ENSP00000422679
ENST00000506163 ENSP00000424926
ENST00000518504
ENST00000507905 ENSP00000430657
ENST00000513228
ENST00000510679
Interactions
Number of Interactions This gene and/or its encoded proteins are associated with 330 experimentally validated interaction(s) in this database.
Experimentally validated
Total 330 [view]
Protein-Protein 329 [view]
Protein-DNA 0
Protein-RNA 0
DNA-DNA 1 [view]
RNA-RNA 0
DNA-RNA 0
Gene Ontology

Molecular Function
Accession GO Term
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0042802 identical protein binding
Biological Process
GO:0000245 spliceosomal complex assembly
GO:0000387 spliceosomal snRNP assembly
GO:0006397 mRNA processing
GO:0007399 nervous system development
GO:0008219 cell death
GO:0010467 gene expression
GO:0016070 RNA metabolic process
GO:0034660 ncRNA metabolic process
GO:0042307 positive regulation of protein import into nucleus
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0015030 Cajal body
GO:0030018 Z disc
GO:0032797 SMN complex
GO:0034719 SMN-Sm protein complex
GO:0097504 Gemini of coiled bodies
Orthologs
No orthologs found for this gene
Pathways
NETPATH
REACTOME
REACT_11066
snRNP Assembly pathway
REACT_11052
Metabolism of non-coding RNA pathway
REACT_71
Gene Expression pathway
KEGG
hsa03013
RNA transport pathway
INOH
PID NCI
Cross-References
SwissProt
TrEMBL
UniProt Splice Variant
Entrez Gene
UniGene Hs.535788
RefSeq NM_000344 NM_001297715 NM_022874 XM_006714677
HUGO
OMIM
CCDS CCDS34181 CCDS34182 CCDS75256
HPRD 02646
IMGT
EMBL
GenPept
RNA Seq Atlas

If you use InnateDB for your research, please cite the following publication:

Breuer et al., InnateDB: systems biology of innate immunity and beyond - recent updates and continuing curation. Nucl. Acids Res. (2013) 41 (D1) 

InnateDB is being developed jointly by the Brinkman Laboratory (Simon Fraser University, British Columbia, Canada), the Hancock Laboratory (University of British Columbia, Vancouver, British Columbia) and the Lynn EMBL Australia Group (South Australian Health & Medical Research Institute and Flinders University, Adelaide, Australia).

Funding is currently provided by Allergen and EMBL Australia. Previous funding has been provided by Genome Canada, the Foundation for the National Institutes of Health through the Grand Challenges in Global Health initiative and by Teagasc. InnateDB curated interactions are licensed under the Design Science License. All other data is licensed under the terms of the originating database. Contact: innatedb-mail@sfu.ca