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    SMN1 survival of motor neuron 1, telomeric [ Homo sapiens (human) ]

    Gene ID: 6606, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SMN1provided by HGNC
    Official Full Name
    survival of motor neuron 1, telomericprovided by HGNC
    Primary source
    HGNC:HGNC:11117
    See related
    Ensembl:ENSG00000172062 MIM:600354; AllianceGenome:HGNC:11117
    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
    SMA; SMN; SMA1; SMA2; SMA3; SMA4; SMA@; SMNT; BCD541; GEMIN1; TDRD16A; T-BCD541
    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. 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]
    Expression
    Ubiquitous expression in bone marrow (RPKM 24.8), testis (RPKM 21.9) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See SMN1 in Genome Data Viewer
    Location:
    5q13.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (70924941..70966375)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (71381729..71423141)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (70220768..70248842)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene GUSB pseudogene 16 Neighboring gene cadherin 12 pseudogene 1 Neighboring gene mitochondrial import receptor subunit TOM5 homolog Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:70220520-70221452 Neighboring gene small EDRK-rich factor 1A Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:70227603-70228594 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:70228664-70229392 Neighboring gene survival motor neuron- antisense 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:70260097-70260788 Neighboring gene uncharacterized LOC112267942 Neighboring gene NLR family apoptosis inhibitory protein Neighboring gene NAIP promoter region Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:70362331-70362930 Neighboring gene general transcription factor IIH subunit 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Utility of two SMN1 variants to improve spinal muscular atrophy carrier diagnosis and genetic counselling. Alías L, et al. Eur J Hum Genet, 2018 Oct. PMID 29904179, Free PMC Article
    2. Correlation between deletion patterns of SMN and NAIP genes and the clinical features of spinal muscular atrophy in Indian patients. Dastur RS, et al. Neurol India, 2006 Sep. PMID 16936383
    3. Subtle mutations in the SMN1 gene in Chinese patients with SMA: p.Arg288Met mutation causing SMN1 transcript exclusion of exon7. Yu-Jin Q, et al. BMC Med Genet, 2012 Sep 20. PMID 22994313, Free PMC Article
    4. SMN, the product of the spinal muscular atrophy-determining gene, is expressed widely but selectively in the developing human forebrain. Briese M, et al. J Comp Neurol, 2006 Aug 10. PMID 16786553
    5. Neuronal-specific roles of the survival motor neuron protein: evidence from survival motor neuron expression patterns in the developing human central nervous system. Giavazzi A, et al. J Neuropathol Exp Neurol, 2006 Mar. PMID 16651888

    See all (465) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Multidisciplinary approach on divergent outcomes in spinal muscular atrophies: comparing DYNC1H1 and SMN1 gene mutations.
      Title: Multidisciplinary approach on divergent outcomes in spinal muscular atrophies: comparing DYNC1H1 and SMN1 gene mutations.
    2. Effect of E134K pathogenic mutation of SMN protein on SMN-SmD1 interaction, with implication in spinal muscular atrophy: A molecular dynamics study.
      Title: Effect of E134K pathogenic mutation of SMN protein on SMN-SmD1 interaction, with implication in spinal muscular atrophy: A molecular dynamics study.
    3. Rare homozygous disease-associated sequence variants in children with spinal muscular atrophy: a phenotypic description and review of the literature.
      Title: Rare homozygous disease-associated sequence variants in children with spinal muscular atrophy: a phenotypic description and review of the literature.
    4. [Analysis of a Chinese pedigree affected with Spinal muscular atrophy due to compound heterozygous variants of SMN gene].
      Title: [Analysis of a Chinese pedigree affected with Spinal muscular atrophy due to compound heterozygous variants of SMN gene].
    5. SMN deficiency perturbs monoamine neurotransmitter metabolism in spinal muscular atrophy.
      Title: SMN deficiency perturbs monoamine neurotransmitter metabolism in spinal muscular atrophy.
    6. SMN haploinsufficiency promotes ischemia/ reperfusion-induced AKI-to-CKD transition by endoplasmic reticulum stress activation.
      Title: SMN haploinsufficiency promotes ischemia/ reperfusion-induced AKI-to-CKD transition by endoplasmic reticulum stress activation.
    7. Deletions of SMNI gene exon 7 and NAIP gene exon 5 in spinal muscular atrophy patients in selected population.
      Title: Deletions of SMNI gene exon 7 and NAIP gene exon 5 in spinal muscular atrophy patients in selected population.
    8. SMN regulates GEMIN5 expression and acts as a modifier of GEMIN5-mediated neurodegeneration.
      Title: SMN regulates GEMIN5 expression and acts as a modifier of GEMIN5-mediated neurodegeneration.
    9. The Carrier Frequency of Two SMN1 Genes in Parents of Symptomatic Children with SMA and the Significance of SMN1 Exon 8 in Carriers.
      Title: The Carrier Frequency of Two SMN1 Genes in Parents of Symptomatic Children with SMA and the Significance of SMN1 Exon 8 in Carriers.
    10. Full-Length SMN Transcript in Extracellular Vesicles as Biomarker in Individuals with Spinal Muscular Atrophy Type 2 Treated with Nusinersen.
      Title: Full-Length SMN Transcript in Extracellular Vesicles as Biomarker in Individuals with Spinal Muscular Atrophy Type 2 Treated with Nusinersen.
    Submit: New GeneRIF Correction See all GeneRIFs (264)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat enhances vIL-6-induced angiogenesis and tumorigenesis of fibroblasts and human endothelial cells, which correlates with upregulation of CD31, CD34, SMA, VEGF, b-FGF, and cyclin D1 expression PubMed
    Vpr vpr HIV-1 Vpr downregulates SMN1 in HeLa cells within 12 hours of exposure PubMed
    Vpu vpu HIV-1 Vpu-expressing U937 monocytes coculture with LX2 stellate cells to upregulate expression of profibrogenic markers COL-1, PCT, SMA-1, VEGF, and MMP2, which is inhibited by MIF treatment PubMed
    matrix gag HIV-1 MA-induced upregulation of collagen-I and alpha-SMA expression is dependent on CXCR2 via the Rho/ROCK-1 pathway PubMed
    gag Treatment of human stellate cells with HIV-1 MA upregulates the expression of CXCR2, syndecan-2, collagen-I, alpha-SMA, vimentin, and endothelin-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA-templated transcription termination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spliceosomal complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in spliceosomal complex assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in spliceosomal snRNP assembly EXP
    Inferred from Experiment
    more info
    		 PubMed 
    involved_in spliceosomal snRNP assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spliceosomal snRNP assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in Cajal body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Cajal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in Gemini of coiled bodies IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Gemini of coiled bodies IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of SMN complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of SMN complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of SMN complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of SMN-Sm protein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Z disc IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in axon IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in neuron projection IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perikaryon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    survival motor neuron protein
    Names
    component of gems 1
    gemin-1
    survival motor neuron 1 protein
    tudor domain containing 16A

    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.

    Genomic

    1. NG_008691.1 RefSeqGene

      Range
      5001..33072
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_676

    mRNA and Protein(s)

    1. NM_000344.4 → NP_000335.1  survival motor neuron protein isoform d

      See identical proteins and their annotated locations for NP_000335.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (d) represents the longest transcript and encodes the longest isoform (d). This variant is thought to be the predominant transcript produced by this copy of the gene.
      Source sequence(s)
      AC044797, AC139834, BC062723
      Consensus CDS
      CCDS34181.1
      UniProtKB/Swiss-Prot
      A8K0V4, Q13119, Q16637, Q549U5, Q96J51
      Related
      ENSP00000370083.4, ENST00000380707.9
      Conserved Domains (1) summary
      pfam06003
      Location:27 → 291
      SMN; Survival motor neuron protein (SMN)

    2. NM_001297715.1 → NP_001284644.1  survival motor neuron protein isoform a

      See identical proteins and their annotated locations for NP_001284644.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (a) lacks the penultimate exon, which results in an alternate translation stop codon, compared to variant d. The resulting isoform (a) is shorter and has a distinct C-terminus, compared to isoform d.
      Source sequence(s)
      AC044797, AC139834
      Consensus CDS
      CCDS75256.1
      Related
      ENSP00000424926.1, ENST00000506163.5
      Conserved Domains (1) summary
      pfam06003
      Location:27 → 278
      SMN; Survival motor neuron protein (SMN)

    3. NM_022874.2 → NP_075012.1  survival motor neuron protein isoform b

      See identical proteins and their annotated locations for NP_075012.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (b) lacks an alternate in-frame exon in the 3' CDS compared to variant d. The resulting protein (isoform b) is shorter but has the same N- and C- termini compared to isoform d.
      Source sequence(s)
      AC139834, BC062723
      Consensus CDS
      CCDS34182.1
      Conserved Domains (1) summary
      pfam06003
      Location:27 → 259
      SMN; Survival motor neuron protein (SMN)

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      70924941..70966375
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417615.1 → XP_047273571.1  survival motor neuron protein isoform X1

    2. XM_017009786.2 → XP_016865275.1  survival motor neuron protein isoform X4

      Conserved Domains (2) summary
      smart00333
      Location:90 → 147
      TUDOR; Tudor domain
      pfam06003
      Location:27 → 246
      SMN; Survival motor neuron protein (SMN)

    3. XM_011543597.2 → XP_011541899.1  survival motor neuron protein isoform X5

      See identical proteins and their annotated locations for XP_011541899.1

      UniProtKB/TrEMBL
      B4DP61
      Related
      ENSP00000423298.1, ENST00000514951.5
      Conserved Domains (1) summary
      pfam06003
      Location:27 → 224
      SMN; Survival motor neuron protein (SMN)

    4. XM_047417618.1 → XP_047273574.1  survival motor neuron protein isoform X6

    5. XM_047417616.1 → XP_047273572.1  survival motor neuron protein isoform X3

      Related
      ENSP00000428128.1, ENST00000503079.6

    6. XM_011543596.2 → XP_011541898.1  survival motor neuron protein isoform X2

      See identical proteins and their annotated locations for XP_011541898.1

      UniProtKB/TrEMBL
      E7EQZ4
      Related
      ENSP00000486539.1, ENST00000625245.2
      Conserved Domains (2) summary
      smart00333
      Location:90 → 147
      TUDOR; Tudor domain
      pfam06003
      Location:27 → 278
      SMN; Survival motor neuron protein (SMN)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791777.1 Reference GRCh38.p14 PATCHES

      Range
      1515739..1557047 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047443291.1 → XP_047299247.1  survival motor neuron protein isoform X1

    2. XM_047443295.1 → XP_047299251.1  survival motor neuron protein isoform X9

    3. XM_047443301.1 → XP_047299257.1  survival motor neuron protein isoform X11

    4. XM_047443298.1 → XP_047299254.1  survival motor neuron protein isoform X10

    5. XM_047443297.1 → XP_047299253.1  survival motor neuron protein isoform X4

    6. XM_047443294.1 → XP_047299250.1  survival motor neuron protein isoform X8

    7. XM_047443303.1 → XP_047299259.1  survival motor neuron protein isoform X13

    8. XM_047443300.1 → XP_047299256.1  survival motor neuron protein isoform X6

    9. XM_047443296.1 → XP_047299252.1  survival motor neuron protein isoform X3

    10. XM_047443292.1 → XP_047299248.1  survival motor neuron protein isoform X7

      UniProtKB/Swiss-Prot
      A8K0V4, Q13119, Q16637, Q549U5, Q96J51

    11. XM_047443302.1 → XP_047299258.1  survival motor neuron protein isoform X12

    12. XM_047443299.1 → XP_047299255.1  survival motor neuron protein isoform X5

      UniProtKB/TrEMBL
      B4DP61

    13. XM_047443293.1 → XP_047299249.1  survival motor neuron protein isoform X2

      UniProtKB/TrEMBL
      E7EQZ4

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003315917.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      439160..485846 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329540.1 → XP_054185515.1  survival motor neuron protein isoform X1

    2. XM_054329545.1 → XP_054185520.1  survival motor neuron protein isoform X14

    3. XM_054329544.1 → XP_054185519.1  survival motor neuron protein isoform X6

    4. XM_054329543.1 → XP_054185518.1  survival motor neuron protein isoform X5

      UniProtKB/TrEMBL
      B4DP61

    5. XM_054329542.1 → XP_054185517.1  survival motor neuron protein isoform X4

    6. XM_054329541.1 → XP_054185516.1  survival motor neuron protein isoform X2

      UniProtKB/TrEMBL
      E7EQZ4

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_187651.1 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      473376..520059
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329962.1 → XP_054185937.1  survival motor neuron protein isoform X1

    2. XM_054329964.1 → XP_054185939.1  survival motor neuron protein isoform X9

    3. XM_054329966.1 → XP_054185941.1  survival motor neuron protein isoform X10

    4. XM_054329969.1 → XP_054185944.1  survival motor neuron protein isoform X11

    5. XM_054329965.1 → XP_054185940.1  survival motor neuron protein isoform X4

    6. XM_054329967.1 → XP_054185942.1  survival motor neuron protein isoform X5

      UniProtKB/TrEMBL
      B4DP61

    7. XM_054329968.1 → XP_054185943.1  survival motor neuron protein isoform X6

    8. XM_054329963.1 → XP_054185938.1  survival motor neuron protein isoform X2

      UniProtKB/TrEMBL
      E7EQZ4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      71381729..71423141
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353282.1 → XP_054209257.1  survival motor neuron protein isoform X1

    2. XM_054353284.1 → XP_054209259.1  survival motor neuron protein isoform X15

    3. XM_054353286.1 → XP_054209261.1  survival motor neuron protein isoform X16

    4. XM_054353289.1 → XP_054209264.1  survival motor neuron protein isoform X17

    5. XM_054353285.1 → XP_054209260.1  survival motor neuron protein isoform X4

    6. XM_054353287.1 → XP_054209262.1  survival motor neuron protein isoform X5

      UniProtKB/TrEMBL
      B4DP61

    7. XM_054353288.1 → XP_054209263.1  survival motor neuron protein isoform X6

    8. XM_054353290.1 → XP_054209265.1  survival motor neuron protein isoform X18

    9. XM_054353291.1 → XP_054209266.1  survival motor neuron protein isoform X19

    10. XM_054353283.1 → XP_054209258.1  survival motor neuron protein isoform X2

      UniProtKB/TrEMBL
      E7EQZ4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q16637.1 GenPept UniProtKB/Swiss-Prot:Q16637

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