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

Gene ID: 6606, updated on 5-Mar-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
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Genomic context

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Location:
5q13.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (70924941..70966375)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (71381729..71423141)
105.20220307 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. Full-Length SMN Transcript in Extracellular Vesicles as Biomarker in Individuals with Spinal Muscular Atrophy Type 2 Treated with Nusinersen. Trifunov S, et al. J Neuromuscul Dis, 2023. PMID 37038823, Free PMC Article
  2. The RNA-Binding Protein SMN as a Novel Player in Laryngeal Squamous Cell Carcinoma. Gabanella F, et al. Int J Mol Sci, 2023 Jan 16. PMID 36675308, Free PMC Article
  3. SMA-linked SMN mutants prevent phase separation properties and SMN interactions with FMRP family members. Binda O, et al. Life Sci Alliance, 2023 Jan. PMID 36375840, Free PMC Article
  4. Internal Introns Promote Backsplicing to Generate Circular RNAs from Spinal Muscular Atrophy Gene. Luo D, et al. Genes (Basel), 2022 Jun 25. PMID 35885927, Free PMC Article
  5. Comprehensive Analysis of Spinal Muscular Atrophy: SMN1 Copy Number, Intragenic Mutation, and 2 + 0 Carrier Analysis by Third-Generation Sequencing. Li S, et al. J Mol Diagn, 2022 Sep. PMID 35659528

See all (446) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. [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].
  2. SMN deficiency perturbs monoamine neurotransmitter metabolism in spinal muscular atrophy.
    Title: SMN deficiency perturbs monoamine neurotransmitter metabolism in spinal muscular atrophy.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. Newborn screening for spinal muscular atrophy in Osaka -challenges in a Japanese pilot study.
    Title: Newborn screening for spinal muscular atrophy in Osaka -challenges in a Japanese pilot study.
  9. SMN Deficiency Destabilizes ABCA1 Expression in Human Fibroblasts: Novel Insights in Pathophysiology of Spinal Muscular Atrophy.
    Title: SMN Deficiency Destabilizes ABCA1 Expression in Human Fibroblasts: Novel Insights in Pathophysiology of Spinal Muscular Atrophy.
  10. The RNA-Binding Protein SMN as a Novel Player in Laryngeal Squamous Cell Carcinoma.
    Title: The RNA-Binding Protein SMN as a Novel Player in Laryngeal Squamous Cell Carcinoma.
Submit: New GeneRIF Correction See all GeneRIFs (261)

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)

Genotypes

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_2023_10

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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