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

    Gene ID: 6606, updated on 11-Jun-2017
    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; Vega:OTTHUMG00000099361
    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]
    Orthologs
    Location:
    5q13.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 5 NC_000005.10 (70924941..70953015)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (70220768..70248839)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene cadherin 12 pseudogene 1 Neighboring gene mitochondrial import receptor subunit TOM5 homolog pseudogene Neighboring gene small EDRK-rich factor 1A Neighboring gene NLR family apoptosis inhibitory protein Neighboring gene general transcription factor IIH subunit 2 Neighboring gene occludin pseudogene

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    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
    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

    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • Metabolism of non-coding RNA, organism-specific biosystem (from REACTOME)
      Metabolism of non-coding RNA, organism-specific biosystemThe term non-coding is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. There is considerable evidence tha...
    • RNA transport, organism-specific biosystem (from KEGG)
      RNA transport, organism-specific biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
    • RNA transport, conserved biosystem (from KEGG)
      RNA transport, conserved biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
    • Survival motor neuron (SMN) complex, organism-specific biosystem (from KEGG)
      Survival motor neuron (SMN) complex, organism-specific biosystemStructural complex; Genetic information processing; RNA processing
    • Survival motor neuron (SMN) complex, conserved biosystem (from KEGG)
      Survival motor neuron (SMN) complex, conserved biosystemStructural complex; Genetic information processing; RNA processing
    • snRNP Assembly, organism-specific biosystem (from REACTOME)
      snRNP Assembly, organism-specific biosystemSmall nuclear ribonucleoproteins (snRNPs) are crucial for pre-mRNA processing to mRNAs. Each snRNP contains a small nuclear RNA (snRNA) and an extremely stable core of seven Sm proteins. The U6 snRNA...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    DNA-templated transcription, termination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    nuclear import TAS
    Traceable Author Statement
    more info
     
    spliceosomal complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    spliceosomal complex assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    spliceosomal snRNP assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    spliceosomal snRNP assembly TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    Cajal body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Gemini of coiled bodies IDA
    Inferred from Direct Assay
    more info
    PubMed 
    SMN complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    SMN-Sm protein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Z disc IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasmic ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
     
    host cell IEA
    Inferred from Electronic Annotation
    more info
     
    neuron projection IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perikaryon IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    survival motor neuron protein
    Names
    component of gems 1
    gemin-1
    survival motor neuron 1 protein
    tudor domain containing 16A

    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_000344.3NP_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)
      AC139834, BC062723
      Consensus CDS
      CCDS34181.1
      UniProtKB/Swiss-Prot
      Q16637
      Related
      ENSP00000370083.4, OTTHUMP00000125198, ENST00000380707.8, OTTHUMT00000216805
      Conserved Domains (2) summary
      smart00333
      Location:90147
      TUDOR; Tudor domain
      pfam06003
      Location:27291
      SMN; Survival motor neuron protein (SMN)
    2. NM_001297715.1NP_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
      UniProtKB/Swiss-Prot
      Q16637
      Related
      ENSP00000424926.1, OTTHUMP00000224066, ENST00000506163.5, OTTHUMT00000373721
      Conserved Domains (2) summary
      smart00333
      Location:90147
      TUDOR; Tudor domain
      pfam06003
      Location:27278
      SMN; Survival motor neuron protein (SMN)
    3. NM_022874.2NP_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
      UniProtKB/Swiss-Prot
      Q16637
      Related
      ENSP00000428128.1, OTTHUMP00000226924, ENST00000503079.6, OTTHUMT00000379154
      Conserved Domains (2) summary
      smart00333
      Location:90147
      TUDOR; Tudor domain
      pfam06003
      Location:27259
      SMN; Survival motor neuron protein (SMN)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p7 Primary Assembly

      Range
      70924941..70953015
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011543598.2XP_011541900.1  survival motor neuron protein isoform X4

      See identical proteins and their annotated locations for XP_011541900.1

      Conserved Domains (1) summary
      pfam06003
      Location:27192
      SMN; Survival motor neuron protein (SMN)
    2. XM_011543597.1XP_011541899.1  survival motor neuron protein isoform X3

      See identical proteins and their annotated locations for XP_011541899.1

      UniProtKB/TrEMBL
      B4DP61
      Related
      ENSP00000423298.1, OTTHUMP00000223567, ENST00000514951.5, OTTHUMT00000372642
      Conserved Domains (1) summary
      pfam06003
      Location:27224
      SMN; Survival motor neuron protein (SMN)
    3. XM_017009786.1XP_016865275.1  survival motor neuron protein isoform X2

      UniProtKB/Swiss-Prot
      Q16637
      Conserved Domains (2) summary
      smart00333
      Location:90147
      TUDOR; Tudor domain
      pfam06003
      Location:27246
      SMN; Survival motor neuron protein (SMN)
    4. XM_011543596.1XP_011541898.1  survival motor neuron protein isoform X1

      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:90147
      TUDOR; Tudor domain
      pfam06003
      Location:27278
      SMN; Survival motor neuron protein (SMN)

    Reference GRCh38.p7 ALT_REF_LOCI_1

    Genomic

    1. NW_003315917.2 Reference GRCh38.p7 ALT_REF_LOCI_1

      Range
      457779..485846 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_2

    Genomic

    1. NT_187651.1 Reference GRCh38.p7 ALT_REF_LOCI_2

      Range
      473376..501444
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018916.2 Alternate CHM1_1.1

      Range
      69671936..69700004
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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