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SMN1 Gene

protein-coding   GIFtS: 67
GCID: GC05P070220

Survival Of Motor Neuron 1, Telomeric

(Previous names: spinal muscular atrophy (Werdnig-Hoffmann disease, Kugelberg-Welander...)
(Previous symbols: SMA@, SMA)
  See SMN1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Survival Of Motor Neuron 1, Telomeric1 2     SMA42 5
SMA1 2     Spinal Muscular Atrophy (Werdnig-Hoffmann Disease, Kugelberg-Welander
Disease)1
SMA@1 2     BCD5412
gemin-11 2     GEMIN12
Tudor Domain Containing 16A1 2     T-BCD5412
Component Of Gems 12 3     TDRD16A2
SMN2 3     Survival Motor Neuron 1 Protein2
SMNT2 3     Survival Motor Neuron Protein2
SMA12 5     Gemin-13
SMA22 5     SMNC3
SMA32 5     

External Ids:    HGNC: 111171   Entrez Gene: 66062   Ensembl: ENSG000001720627   OMIM: 6003545   UniProtKB: Q166373   

Export aliases for SMN1 gene to outside databases

Previous GC identifers: GC05M069123 GC05M070536 GC05M069032 GC05M069077 GC05P069381 GC05P070257 GC05P065882


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SMN1 Gene:
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)

GeneCards Summary for SMN1 Gene:
SMN1 (survival of motor neuron 1, telomeric) is a protein-coding gene. Diseases associated with SMN1 include werdnig-hoffmann disease, and muscular atrophy. An important paralog of this gene is SMN2.

UniProtKB/Swiss-Prot: SMN_HUMAN, Q16637
Function: The SMN complex plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the
building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most
spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG
that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the
cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by
the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from
the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their
transport to the nucleus. Ensures the correct splicing of U12 intron-containing genes that may be important for
normal motor and proprioceptive neurons development. May also play a role in the metabolism of small nucleolar
ribonucleoprotein (snoRNPs)

Gene Wiki entry for SMN1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NT_187651.1  NC_000005.9  NT_034772.7  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SMN1 gene promoter:
         CREB   C/EBPbeta   deltaCREB   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSMN1 promoter sequence
   Search Chromatin IP Primers for SMN1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMN1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q13.2   Ensembl cytogenetic band:  5q13.2   HGNC cytogenetic band: 5q13.2

SMN1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMN1 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P070220:  view genomic region     (about GC identifiers)

Start:
70,220,768 bp from pter      End:
70,249,769 bp from pter
Size:
29,002 bases      Orientation:
plus strand

1 alternative location:
Chr5-,NW_003315917.2 457,779-485,846     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SMN_HUMAN, Q16637 (See protein sequence)
Recommended Name: Survival motor neuron protein  
Size: 294 amino acids; 31849 Da
Subunit: Homodimer. Part of the core SMN complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5,
GEMIN6, GEMIN7, GEMIN8 and STRAP/UNRIP. Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3,
GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE,
SNRPF and SNRPG. Component of an import snRNP complex composed of KPNB1, RNUT1, SMN1 and ZNF259. Interacts with
DDX20, FBL, NOLA1, RNUT1, SYNCRIP and with several spliceosomal snRNP core Sm proteins, including SNRPB, SNRPD1,
SNRPD2, SNRPD3, SNRPE and ILF3. Interacts with OSTF1, LSM10, LSM11 and RPP20/POP7
Miscellaneous: The SMN gene is present in two highly homologous and functional copies (TelSMN/SMN1 and
CenSMN/SMN2). The telomeric copy of SMN gene (TelSMN/SMN1) seems to be the SMA-determining gene while the
centromeric copy seems unaffected
Selected PDB 3D structures from and Proteopedia for SMN1 (see all 7):
1G5V (3D)        1MHN (3D)        2LEH (3D)        3S6N (3D)        4A4E (3D)        4A4G (3D)    
Secondary accessions: A8K0V4 Q13119 Q549U5 Q96J51
Alternative splicing: 4 isoforms:  Q16637-1   Q16637-2   Q16637-3   Q16637-4   (Thought to be a non-functional protein that lacks the capacity to oligomerize and thus cannot interact with Sm proteins. Primarily derived from SMN2 gene)

Explore the universe of human proteins at neXtProt for SMN1: NX_Q16637

Explore proteomics data for SMN1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys41, Lys51, Lys186
  • Modification sites at PhosphoSitePlus

  • See SMN1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_000335.1  NP_075012.1  

    ENSEMBL proteins: 
     ENSP00000428128   ENSP00000370083   ENSP00000423298   ENSP00000422679   ENSP00000424926  
     ENSP00000430657   ENSP00000305857  
    Reactome Protein details: Q16637

    SMN1 Human Recombinant Protein Products:

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    Search eBioscience for ELISAs for SMN1 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    TDRD: Tudor domain containing

    2 InterPro protein domains:
     IPR010304 Survival_motor_neuron
     IPR002999 Tudor

    Graphical View of Domain Structure for InterPro Entry Q16637

    ProtoNet protein and cluster: Q16637

    2 Blocks protein domains:
    IPB002999 Tudor domain
    IPB010304 Survival motor neuron


    UniProtKB/Swiss-Prot: SMN_HUMAN, Q16637
    Domain: The Tudor domain mediates association with dimethylarginines, which are common in snRNP proteins
    Similarity: Belongs to the SMN family
    Similarity: Contains 1 Tudor domain


    Find genes that share domains with SMN1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SMN_HUMAN, Q16637
    Function: The SMN complex plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the
    building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most
    spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG
    that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the
    cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by
    the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from
    the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their
    transport to the nucleus. Ensures the correct splicing of U12 intron-containing genes that may be important for
    normal motor and proprioceptive neurons development. May also play a role in the metabolism of small nucleolar
    ribonucleoprotein (snoRNPs)

         Genatlas biochemistry entry for SMN1:
    survival motor neuron,telomeric copy;predominant by expressed in fetal tissues generally located both in the
    cytoplasm and the nucleus,where it is highly associated with gem-like (gemini of coiled bodies)
    structures,associating with a protein SIP1 to form a complex with several spliceosomal snRNP proteins playing an
    essential role in spliceosomal snRNP biogenesis and pre mRNA splicing regulatory activity in the nucleus and as
    regulator of transcription,with aberrant splicing of exon 7 determining the disease,interacting with BCL2

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003723RNA binding ----
    GO:0005515protein binding ----
    GO:0042802identical protein binding ----
         
    Find genes that share ontologies with SMN1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for SMN1:
     Increased S DNA content 

         Selected MGI mutant phenotypes (inferred from 14 alleles(MGI details for Smn1) (see all 19):
     behavior/neurological  cardiovascular system  cellular  craniofacial  digestive/alimentary 
     embryogenesis  growth/size/body  hearing/vestibular/ear  homeostasis/metabolism  integument 
     limbs/digits/tail  mortality/aging  muscle  nervous system  no phenotypic analysis 

    Find genes that share phenotypes with SMN1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for SMN1: Smn1tm1Hung Smn1tm1.1Jme

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SMN1
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SMN1

    miRNA
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    hsa-mir-30a-5p (MIRT028496), hsa-mir-26b-5p (MIRT029454), hsa-mir-132-3p (MIRT021810)

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    GenScript: all cDNA clones in your preferred vector (see all 2): SMN1 (NM_022874)
    Browse Sino Biological Human cDNA Clones
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SMN_HUMAN, Q16637: Cytoplasm. Nucleus, gem. Cytoplasmic granule. Cytoplasm, myofibril, sarcomere, Z line (By
    similarity). Note=Colocalizes with Actn at the Z-line of skeletal muscle (By similarity). Under stress conditions
    colocalizes with RPP20/POP7 in punctuated cytoplasmic granules
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol4
    extracellular1
    plasma membrane1

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ----
    GO:0005654nucleoplasm ----
    GO:0005681spliceosomal complex ----
    GO:0005737cytoplasm ----
    GO:0005829cytosol ----

    Find genes that share ontologies with SMN1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for SMN1 About    
    See pathways by source

    SuperPathContained pathways About
    1Regulation of Glucokinase by Glucokinase Regulatory Protein
    Metabolism of non-coding RNA0.54
    snRNP Assembly0.54
    2Gene Expression
    Gene Expression0.40
    3Translational Control
    Translational Control
    4RNA transport
    RNA transport


    Find genes that share SuperPaths with SMN1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for SMN1
        Translational Control

    1 Reactome Pathway for SMN1
        snRNP Assembly


    1 Kegg Pathway  (Kegg details for SMN1):
        RNA transport

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SMN1
    Interactions:

        GeneGlobe Interaction Network for SMN1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SMN1 (Q166371, 2, 3 ENSP000003700834) via UniProtKB, MINT, STRING, and/or I2D (see all 985)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053, ENSP000003529804I2D: score=1 STRING: ENSP00000352980
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000245spliceosomal complex assembly ----
    GO:0000387spliceosomal snRNP assembly ----
    GO:0006397mRNA processing ----
    GO:0007399nervous system development ----
    GO:0008219cell death ----

    Find genes that share ontologies with SMN1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SMN1 (SMN)

    Selected Novoseek inferred chemical compound relationships for SMN1 gene (see all 11)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    phenylbutyrate 73.3 6 15523494 (3), 14560316 (2), 18633133 (1)
    gemini 55.3 1 14697339 (1)
    valproic acid 49.2 17 14595654 (3), 16611218 (2), 12915451 (2), 19733665 (2) (see all 8)
    aclarubicin 29.1 1 11734549 (1)
    aminoglycosides 19.4 8 15790598 (2), 16951947 (2), 19625298 (1), 19150990 (1)
    valproate 16.8 3 16607616 (1), 16775228 (1), 18633133 (1)
    oligonucleotide 11.9 6 9987714 (1), 16449646 (1), 17647030 (1), 19535574 (1)
    ribonucleic acid 10 2 17761657 (2)
    arginine 8.02 13 12244096 (4), 11720283 (1), 12486110 (1), 11389857 (1) (see all 8)
    tyrosine 1.54 1 9158159 (1)



    Find genes that share compounds with SMN1           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SMN1 gene (2 alternative transcripts): 
    NM_000344.3  NM_022874.2  

    Unigene Cluster for SMN1:

    Survival of motor neuron 1, telomeric
    Hs.535788  [show with all ESTs]
    Unigene Representative Sequence: NM_000344
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000503079 ENST00000380707(uc003kak.3 uc003kam.3) ENST00000514951(uc011crr.2)
    ENST00000506239 ENST00000506163 ENST00000518504 ENST00000507905 ENST00000513228
    ENST00000510679 ENST00000351205(uc003kal.3 uc003kan.3)
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      QuantiFast Probe-based Assays in human, mouse, rat SMN1

    Additional mRNA sequence: 

    AK298203.1 BC062723.1 JQ657798.1 JQ657799.1 JQ657800.1 JQ657801.1 JQ657802.1 JQ657803.1 
    JQ690867.1 JQ690868.1 JQ732166.1 JQ732167.1 JQ745297.1 U18423.1 

    16 DOTS entries:

    DT.91752366  DT.100810925  DT.100799306  DT.100810924  DT.95367668  DT.91752362  DT.100018657  DT.100810926 
    DT.99958452  DT.100661323  DT.100810917  DT.120845147  DT.100708213  DT.100765329  DT.428244  DT.91693694 

    Selected AceView cDNA sequences (see all 485):

    BM792538 BG028018 BC015308 AA916956 AI825654 CA748695 CB306328 AI702752 
    BM804381 AI762053 BI496007 AV727787 BI334409 NM_022978 AA740388 CA426506 
    BM672905 BX642318 AI367511 AA973579 AI247115 AV702489 AL702418 CA313754 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SMN1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCTGTTCATT
    SMN1 Expression
    About this image


    SMN1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Skeletal Muscle (Muscoskeletal System)    fully expand to see all 2 entries
             Mononuclear Myocytes Hyoid Arch Muscles
     
     Limb (Muscoskeletal System)
             Limb Bud
    SMN1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SMN1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.535788

    UniProtKB/Swiss-Prot: SMN_HUMAN, Q16637
    Tissue specificity: Expressed in a wide variety of tissues. Expressed at high levels in brain, kidney and liver,
    moderate levels in skeletal and cardiac muscle, and low levels in fibroblasts and lymphocytes. Also seen at high
    levels in spinal cord. Present in osteoclasts and mononuclear cells (at protein level)

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for SMN1 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Smn11 , 5 survival motor neuron 11, 5 83.81(n)1
    82.86(a)1
      13 (52.99 cM)5
    205951  NM_011420.21  NP_035550.11 
     1001248525 
    chicken
    (Gallus gallus)
    Aves SMN1 survival of motor neuron 65.35(n)
    62.56(a)
      374025  NM_204199.1  NP_989530.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    62(a)
    1 → many
    2(16889501-16899457)
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3984382 hypothetical protein LOC398438 75.59(n)    BC045073.1 
    zebrafish
    (Danio rerio)
    Actinopterygii smn2 survival motor neuron 77.81(n)   30432  BC060942.1 
    worm
    (Caenorhabditis elegans)
    Secernentea smn-16
    Protein SMN-1, isoform a (smn-1) mRNA, complete cd...
    31(a)
    1 → many
    I(9511190-9512139) WBGene00004887


    ENSEMBL Gene Tree for SMN1 (if available)
    TreeFam Gene Tree for SMN1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SMN1 gene
    SMN21 2  
    2 SIMAP similar genes for SMN1 using alignment to 8 protein entries:     SMN_HUMAN (see all proteins):
    SMN    SMN2

    Find genes that share paralogs with SMN1           About GenesLikeMe


    2 Pseudogenes.org Pseudogenes for SMN1
    PGOHUM00000245781 PGOHUM00000236401


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SMN1 (see all 83)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0348094
    Spinal muscular atrophy 3 (SMA3)4--see VAR_0348092 S G mis40--------
    VAR_0348064
    Spinal muscular atrophy 2 (SMA2)4--see VAR_0348062 A G mis40--------
    VAR_0100514
    Spinal muscular atrophy 3 (SMA3)4--see VAR_0100512 P L mis40--------
    VAR_0056184
    Spinal muscular atrophy 3 (SMA3)4--see VAR_0056182 T I mis40--------
    VAR_0056174
    Spinal muscular atrophy 1 (SMA1)4--see VAR_0056172 Y C mis40--------
    VAR_0348044
    Spinal muscular atrophy 3 (SMA3)4--see VAR_0348042 D V mis40--------
    VAR_0056204
    Spinal muscular atrophy 1 (SMA1)4--see VAR_0056202 G V mis40--------
    VAR_0348034
    Spinal muscular atrophy 2 (SMA2)4--see VAR_0348032 D N mis40--------
    VAR_0348074
    Spinal muscular atrophy 1 (SMA1)4--see VAR_0348072 I F mis40--------
    VAR_0056154
    Spinal muscular atrophy 3 (SMA3)4--see VAR_0056152 A G mis40--------

    HapMap Linkage Disequilibrium report for SMN1 (70220768 - 70249769 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SMN1 (see all 103):    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv19n31CNV Duplication19718026
    nsv471547CNV Duplication19718026
    nsv471433CNV Duplication19718026
    nsv507261CNV Insertion20534489
    dgv6149n71CNV Loss21882294
    nsv881768CNV Loss21882294
    dgv6144n71CNV Loss21882294
    nsv821643CNV Loss15273396
    nsv882115CNV Loss21882294
    dgv6101n71CNV Loss21882294

    Human Gene Mutation Database (HGMD): SMN1
    Locus Specific Mutation Databases (LSDB): SMN1

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 600354   
    OMIM disorders: 253300  253550  253400  271150  
    UniProtKB/Swiss-Prot: SMN_HUMAN, Q16637
  • Spinal muscular atrophy 1 (SMA1) [MIM:253300]: A form of spinal muscular atrophy, a group of
    neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to
    symmetrical muscle weakness and atrophy. Autosomal recessive forms are classified according to the age of onset,
    the maximum muscular activity achieved, and survivorship. The severity of the disease is mainly determined by the
    copy number of SMN2, a copy gene which predominantly produces exon 7-skipped transcripts and only low amount of
    full-length transcripts that encode for a protein identical to SMN1. Only about 4% of SMA patients bear one SMN1
    copy with an intragenic mutation. SMA1 is a severe form, with onset before 6 months of age. SMA1 patients never
    achieve the ability to sit. Note=The disease is caused by mutations affecting the gene represented in this entry
  • Spinal muscular atrophy 2 (SMA2) [MIM:253550]: An autosomal recessive form of spinal muscular atrophy, a
    neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to
    symmetrical muscle weakness and atrophy. It has intermediate severity, with onset between 6 and 18 months.
    Patients do not reach the motor milestone of standing, and survive into adulthood. Note=The disease is caused by
    mutations affecting the gene represented in this entry
  • Spinal muscular atrophy 3 (SMA3) [MIM:253400]: An autosomal recessive form of spinal muscular atrophy, a
    neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to
    symmetrical muscle weakness and atrophy. Onset is after 18 months. Patients develop ability to stand and walk and
    survive into adulthood. Note=The disease is caused by mutations affecting the gene represented in this entry
  • Spinal muscular atrophy 4 (SMA4) [MIM:271150]: An autosomal recessive form of spinal muscular atrophy, a
    neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to
    symmetrical muscle weakness and atrophy. Onset is in adulthood, disease progression is slow, and patients can
    stand and walk. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 18 diseases for SMN1:    
    About MalaCards
    werdnig-hoffmann disease    muscular atrophy    spinal muscular atrophy 1    progressive muscular atrophy
    werdnig-hoffman disease    adult spinal muscular atrophy    juvenile spinal muscular atrophy    anterior horn cell disease
    spinal muscular atrophy with progressive myoclonic epilepsy    spinal muscular atrophy    spinal muscular atrophy type 2    spinal muscular atrophy, type iii, modifier of
    cytoplasmic body myopathy    motor neuron disease    differentiating neuroblastoma    cerebellar ataxia and hypogonadotropic hypogonadism
    proximal spinal muscular atrophy    amyotrophic lateral sclerosis

    4 diseases from the University of Copenhagen DISEASES database for SMN1:
    Muscular atrophy     Motor neuron disease     Neuropathy     Autosomal recessive disease

    Find genes that share disorders with SMN1           About GenesLikeMe

    Selected Novoseek inferred disease relationships for SMN1 gene (see all 30)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    muscular atrophy spinal 99.2 487 17761651 (5), 15964810 (4), 17761649 (3), 17761657 (3) (see all 99)
    werdnig-hoffmann disease 93.1 22 11504604 (2), 9363657 (1), 9719377 (1), 18662980 (1) (see all 19)
    sma iii 92.5 13 8595417 (1), 9713008 (1), 11987841 (1), 8730281 (1) (see all 11)
    sma ii 90 8 8595417 (2), 11287750 (2), 10652743 (1), 16936383 (1) (see all 6)
    neuromuscular diseases 85.6 45 9735373 (1), 10501549 (1), 15832310 (1), 17027862 (1) (see all 40)
    motor neuron disease 79.7 25 19716110 (1), 9259265 (1), 9585359 (1), 11313744 (1) (see all 23)
    spinal disorder 79.1 28 9719377 (1), 11509571 (1), 15964810 (1), 11121410 (1) (see all 25)
    motor neuron disease lower 74.2 6 9585359 (1), 11993528 (1), 18367439 (1), 16931506 (1) (see all 6)
    atrophy 66.8 7 16108074 (1), 19517146 (1), 19351384 (1), 17511908 (1) (see all 7)
    neurodegenerative diseases 63.5 32 11509571 (1), 12878704 (1), 16385450 (1), 12833158 (1) (see all 29)

    GeneTests: SMN1
    GeneReviews: SMN1
    Genetic Association Database (GAD): SMN1
    Human Genome Epidemiology (HuGE) Navigator: SMN1 (34 documents)

    Export disorders for SMN1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SMN1 gene, integrated from 10 sources (see all 570):
    (articles sorted by number of sources associating them with SMN1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of a spinal muscular atrophy- determining gene. (PubMed id 7813012)1, 2, 3 Lefebvre S....Melki J. (Cell 1995)
    2. SMN genotypes producing less SMN protein increase susceptibility to and severity of sporadic ALS. (PubMed id 16093455)1, 4, 9 Veldink J.H....Van den Berg L.H. (Neurology 2005)
    3. Molecular and functional analysis of intragenic SMN1 mutations in patients with spinal muscular atrophy. (PubMed id 15580564)1, 2, 9 Sun Y.... Wirth B. (Hum. Mutat. 2005)
    4. Quantitative studies on SMN1 gene and carrier testing of spinal muscular atrophy. (PubMed id 16331551)1, 4, 9 Chen W.J....Mu-rong S.X. (Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2005)
    5. The survival motor neuron protein in spinal muscular atrophy. (PubMed id 9259265)1, 2, 9 Coovert D.D.... Burghes A.H.M. (Hum. Mol. Genet. 1997)
    6. [Molecular analysis of survival motor neuron gene in 338 suspicious children patients with spinal muscular atrophy]. (PubMed id 19134255)1, 4, 9 Song F....Jin Y.W. (Zhonghua Er Ke Za Zhi 2008)
    7. C117T variant in the SMN1 gene found in the Japanese population. (PubMed id 17250497)1, 4, 9 Sadewa A.H....Nishio H. (Pediatr Int 2007)
    8. Rpp20 interacts with SMN and is re-distributed into SMN granules in response to stress. (PubMed id 14715275)1, 2, 9 Hua Y. and Zhou J. (Biochem. Biophys. Res. Commun. 2004)
    9. Molecular analysis of the SMN1 and NAIP genes in Iranian patients with spinal muscular atrophy. (PubMed id 18071605)1, 4, 9 Derakhshandeh-Peykar P....Farhud D.D. (Ann. Acad. Med. Singap. 2007)
    10. A novel function for SMN, the spinal muscular atrophy disease gene product, in pre-mRNA splicing. (PubMed id 9845364)1, 2, 9 Pellizzoni L.... Dreyfuss G. (Cell 1998)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6606 HGNC: 11117 AceView: SMN1 Ensembl:ENSG00000172062 euGenes: HUgn6606
    ECgene: SMN1 Kegg: 6606 H-InvDB: SMN1

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SMN1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SMN1[genesymbol]
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SMN2[genesymbol]
    SHMPDhttp://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=SMN1

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SMN1 gene:
    Search GeneIP for patents involving SMN1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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