SMN1 Gene

HGNC Family Tudor domain containing (TDRD)
Name survival of motor neuron 1, telomeric
Description 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]
Synonyms BCD541, SMA1, SMA4, SMA@, T-BCD541, SMA, TDRD16A, SMA2, GEMIN1, SMNT
Proteins SMN_HUMAN
NCBI Gene ID 6606
API
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Predicted Functions View SMN1's ARCHS4 Predicted Functions.
Co-expressed Genes View SMN1's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View SMN1's ARCHS4 Predicted Functions.

Functional Associations

SMN1 has 3,062 functional associations with biological entities spanning 8 categories (molecular profile, organism, disease, phenotype or trait, functional term, phrase or reference, chemical, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 66 datasets.

Click the + buttons to view associations for SMN1 from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq tissue samples with high or low expression of SMN1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
BioGPS Mouse Cell Type and Tissue Gene Expression Profiles cell types and tissues with high or low expression of SMN1 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
CCLE Cell Line Gene CNV Profiles cell lines with high or low copy number of SMN1 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
CHEA Transcription Factor Binding Site Profiles transcription factor binding site profiles with transcription factor binding evidence at the promoter of SMN1 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
CHEA Transcription Factor Targets transcription factors binding the promoter of SMN1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
ClinVar Gene-Phenotype Associations phenotypes associated with SMN1 gene from the curated ClinVar Gene-Phenotype Associations dataset.
COMPARTMENTS Curated Protein Localization Evidence Scores cellular components containing SMN1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
COMPARTMENTS Text-mining Protein Localization Evidence Scores cellular components co-occuring with SMN1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
CORUM Protein Complexes protein complexs containing SMN1 protein from the CORUM Protein Complexes dataset.
COSMIC Cell Line Gene CNV Profiles cell lines with high or low copy number of SMN1 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
COSMIC Cell Line Gene Mutation Profiles cell lines with SMN1 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
CTD Gene-Chemical Interactions chemicals interacting with SMN1 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
CTD Gene-Disease Associations diseases associated with SMN1 gene/protein from the curated CTD Gene-Disease Associations dataset.
DEPOD Substrates of Phosphatases phosphatases that dephosphorylate SMN1 protein from the curated DEPOD Substrates of Phosphatases dataset.
DISEASES Curated Gene-Disease Assocation Evidence Scores diseases involving SMN1 gene from the DISEASES Curated Gene-Disease Assocation Evidence Scores dataset.
DISEASES Text-mining Gene-Disease Assocation Evidence Scores diseases co-occuring with SMN1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
ENCODE Histone Modification Site Profiles histone modification site profiles with high histone modification abundance at SMN1 gene from the ENCODE Histone Modification Site Profiles dataset.
ENCODE Transcription Factor Binding Site Profiles transcription factor binding site profiles with transcription factor binding evidence at the promoter of SMN1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
ENCODE Transcription Factor Targets transcription factors binding the promoter of SMN1 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
ESCAPE Omics Signatures of Genes and Proteins for Stem Cells PubMedIDs of publications reporting gene signatures containing SMN1 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
GAD Gene-Disease Associations diseases associated with SMN1 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
GAD High Level Gene-Disease Associations diseases associated with SMN1 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.
GeneRIF Biological Term Annotations biological terms co-occuring with SMN1 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
GeneSigDB Published Gene Signatures PubMedIDs of publications reporting gene signatures containing SMN1 from the GeneSigDB Published Gene Signatures dataset.
GEO Signatures of Differentially Expressed Genes for Kinase Perturbations kinase perturbations changing expression of SMN1 gene from the GEO Signatures of Differentially Expressed Genes for Kinase Perturbations dataset.
GEO Signatures of Differentially Expressed Genes for Small Molecules small molecule perturbations changing expression of SMN1 gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset.
GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations transcription factor perturbations changing expression of SMN1 gene from the GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations dataset.
GEO Signatures of Differentially Expressed Genes for Viral Infections virus perturbations changing expression of SMN1 gene from the GEO Signatures of Differentially Expressed Genes for Viral Infections dataset.
GTEx Tissue Gene Expression Profiles tissues with high or low expression of SMN1 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles dataset.
GTEx Tissue Sample Gene Expression Profiles tissue samples with high or low expression of SMN1 gene relative to other tissue samples from the GTEx Tissue Sample Gene Expression Profiles dataset.
Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles cell lines with high or low expression of SMN1 gene relative to other cell lines from the Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles dataset.
HPA Cell Line Gene Expression Profiles cell lines with high or low expression of SMN1 gene relative to other cell lines from the HPA Cell Line Gene Expression Profiles dataset.
HPA Tissue Gene Expression Profiles tissues with high or low expression of SMN1 gene relative to other tissues from the HPA Tissue Gene Expression Profiles dataset.
HPA Tissue Protein Expression Profiles tissues with high or low expression of SMN1 protein relative to other tissues from the HPA Tissue Protein Expression Profiles dataset.
HPA Tissue Sample Gene Expression Profiles tissue samples with high or low expression of SMN1 gene relative to other tissue samples from the HPA Tissue Sample Gene Expression Profiles dataset.
HPM Cell Type and Tissue Protein Expression Profiles cell types and tissues with high or low expression of SMN1 protein relative to other cell types and tissues from the HPM Cell Type and Tissue Protein Expression Profiles dataset.
HPO Gene-Disease Associations phenotypes associated with SMN1 gene by mapping known disease genes to disease phenotypes from the HPO Gene-Disease Associations dataset.
Hub Proteins Protein-Protein Interactions interacting hub proteins for SMN1 from the curated Hub Proteins Protein-Protein Interactions dataset.
HuGE Navigator Gene-Phenotype Associations phenotypes associated with SMN1 gene by text-mining GWAS publications from the HuGE Navigator Gene-Phenotype Associations dataset.
InterPro Predicted Protein Domain Annotations protein domains predicted for SMN1 protein from the InterPro Predicted Protein Domain Annotations dataset.
JASPAR Predicted Transcription Factor Targets transcription factors regulating expression of SMN1 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Transcription Factor Targets dataset.
KEA Substrates of Kinases kinases that phosphorylate SMN1 protein from the curated KEA Substrates of Kinases dataset.
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles cell lines with high or low copy number of SMN1 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset.
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles cell lines with SMN1 gene mutations from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles dataset.
LOCATE Curated Protein Localization Annotations cellular components containing SMN1 protein in low- or high-throughput protein localization assays from the LOCATE Curated Protein Localization Annotations dataset.
LOCATE Predicted Protein Localization Annotations cellular components predicted to contain SMN1 protein from the LOCATE Predicted Protein Localization Annotations dataset.
MiRTarBase microRNA Targets microRNAs targeting SMN1 gene in low- or high-throughput microRNA targeting studies from the MiRTarBase microRNA Targets dataset.
MPO Gene-Phenotype Associations phenotypes of transgenic mice caused by SMN1 gene mutations from the MPO Gene-Phenotype Associations dataset.
NURSA Protein Complexes protein complexs containing SMN1 protein recovered by IP-MS from the NURSA Protein Complexes dataset.
NURSA Protein-Protein Interactions interacting proteins for SMN1 from the NURSA Protein-Protein Interactions dataset.
OMIM Gene-Disease Associations phenotypes associated with SMN1 gene from the curated OMIM Gene-Disease Associations dataset.
Phosphosite Textmining Biological Term Annotations biological terms co-occuring with SMN1 protein in abstracts of publications describing phosphosites from the Phosphosite Textmining Biological Term Annotations dataset.
ProteomicsDB Cell Type and Tissue Protein Expression Profiles cell types and tissues with high or low expression of SMN1 protein relative to other cell types and tissues from the ProteomicsDB Cell Type and Tissue Protein Expression Profiles dataset.
Reactome Pathways pathways involving SMN1 protein from the Reactome Pathways dataset.
Roadmap Epigenomics Cell and Tissue Gene Expression Profiles cell types and tissues with high or low expression of SMN1 gene relative to other cell types and tissues from the Roadmap Epigenomics Cell and Tissue Gene Expression Profiles dataset.
Roadmap Epigenomics Histone Modification Site Profiles histone modification site profiles with high histone modification abundance at SMN1 gene from the Roadmap Epigenomics Histone Modification Site Profiles dataset.
SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Drugs drug perturbations changing phosphorylation of SMN1 protein from the SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Drugs dataset.
SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Protein Ligands ligand (protein) perturbations changing phosphorylation of SMN1 protein from the SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Protein Ligands dataset.
TargetScan Predicted Nonconserved microRNA Targets microRNAs regulating expression of SMN1 gene predicted using nonconserved miRNA seed sequences from the TargetScan Predicted Nonconserved microRNA Targets dataset.
TCGA Signatures of Differentially Expressed Genes for Tumors tissue samples with high or low expression of SMN1 gene relative to other tissue samples from the TCGA Signatures of Differentially Expressed Genes for Tumors dataset.
TISSUES Curated Tissue Protein Expression Evidence Scores tissues with high expression of SMN1 protein from the TISSUES Curated Tissue Protein Expression Evidence Scores dataset.
TISSUES Experimental Tissue Protein Expression Evidence Scores tissues with high expression of SMN1 protein in proteomics datasets from the TISSUES Experimental Tissue Protein Expression Evidence Scores dataset.
TISSUES Text-mining Tissue Protein Expression Evidence Scores tissues co-occuring with SMN1 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores dataset.
TRANSFAC Predicted Transcription Factor Targets transcription factors regulating expression of SMN1 gene predicted using known transcription factor binding site motifs from the TRANSFAC Predicted Transcription Factor Targets dataset.
Virus MINT Protein-Viral Protein Interactions interacting viral proteins for SMN1 from the Virus MINT Protein-Viral Protein Interactions dataset.
Virus MINT Protein-Virus Interactions viruses interacting with SMN1 from the Virus MINT Protein-Virus Interactions dataset.