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    SMN2 survival of motor neuron 2, centromeric [ Homo sapiens (human) ]

    Gene ID: 6607, updated on 9-Apr-2017
    Official Symbol
    SMN2provided by HGNC
    Official Full Name
    survival of motor neuron 2, centromericprovided by HGNC
    Primary source
    HGNC:HGNC:11118
    See related
    Ensembl:ENSG00000205571 MIM:601627; Vega:OTTHUMG00000099389
    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
    SMNC; BCD541; GEMIN1; TDRD16B; C-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. While mutations in the telomeric copy are associated with spinal muscular atrophy, mutations in this gene, the centromeric copy, do not lead to disease. This gene 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 full length 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. Four transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Sep 2008]
    Orthologs
    Location:
    5q13.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 5 NC_000005.10 (70049523..70077595)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (69345350..69373422)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369228 Neighboring gene cadherin 12 pseudogene 2 Neighboring gene mitochondrial import receptor subunit TOM5 homolog pseudogene Neighboring gene small EDRK-rich factor 1B Neighboring gene NLR family apoptosis inhibitory protein pseudogene Neighboring gene cadherin 12 pseudogene 3 Neighboring gene glucuronidase beta 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?

    • 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

    Clone Names

    • MGC5208, FLJ76644, MGC20996

    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
     
    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
    tudor domain containing 16B

    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_008728.1 RefSeqGene

      Range
      5001..33073
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_017411.3NP_059107.1  survival motor neuron protein isoform d

      See identical proteins and their annotated locations for NP_059107.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (d) represents the longest transcript and encodes the longest isoform (d).
      Source sequence(s)
      AC140134, AI312583, BC015308, CN272420
      Consensus CDS
      CCDS4007.1
      UniProtKB/Swiss-Prot
      Q16637
      Related
      ENSP00000370119.4, OTTHUMP00000125236, ENST00000380743.8, OTTHUMT00000216845
      Conserved Domains (2) summary
      smart00333
      Location:90147
      TUDOR; Tudor domain
      pfam06003
      Location:27291
      SMN; Survival motor neuron protein (SMN)
    2. NM_022875.2NP_075013.1  survival motor neuron protein isoform a

      See identical proteins and their annotated locations for NP_075013.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (a) lacks an alternate exon in the 3' CDS compared to variant d. The resulting protein (isoform a) is shorter and has a distinct C-terminus compared to isoform d. This variant is thought to be the predominant transcript produced by this copy of the gene.
      Source sequence(s)
      AA029652, AC140134, AI312583, BC000908
      Consensus CDS
      CCDS54867.1
      UniProtKB/Swiss-Prot
      Q16637
      Related
      ENSP00000486152.1, OTTHUMP00000279363, ENST00000626847.2, OTTHUMT00000484407
      Conserved Domains (2) summary
      smart00333
      Location:90147
      TUDOR; Tudor domain
      pfam06003
      Location:27278
      SMN; Survival motor neuron protein (SMN)
    3. NM_022876.2NP_075014.1  survival motor neuron protein isoform b

      See identical proteins and their annotated locations for NP_075014.1

      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)
      AC140134, AI312583, BC015308, CN272420
      Consensus CDS
      CCDS4008.1
      UniProtKB/Swiss-Prot
      Q16637
      Related
      ENSP00000370118.4, OTTHUMP00000125237, ENST00000380742.8, OTTHUMT00000216846
      Conserved Domains (2) summary
      smart00333
      Location:90147
      TUDOR; Tudor domain
      pfam06003
      Location:27259
      SMN; Survival motor neuron protein (SMN)
    4. NM_022877.2NP_075015.1  survival motor neuron protein isoform c

      See identical proteins and their annotated locations for NP_075015.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (c) lacks two alternate exons in the 3' CDS compared to variant d. The resulting protein (isoform c) is shorter and has a distinct C-terminus compared to isoform d.
      Source sequence(s)
      AA029652, AC140134, AI312583, BC000908
      UniProtKB/Swiss-Prot
      Q16637
      Conserved Domains (2) summary
      smart00333
      Location:90147
      TUDOR; Tudor domain
      pfam06003
      Location:27246
      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
      70049523..70077595
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011543602.2XP_011541904.1  survival motor neuron protein isoform X5

      See identical proteins and their annotated locations for XP_011541904.1

      Conserved Domains (1) summary
      pfam06003
      Location:27192
      SMN; Survival motor neuron protein (SMN)
    2. XM_011543603.2XP_011541905.1  survival motor neuron protein isoform X6

      See identical proteins and their annotated locations for XP_011541905.1

      Conserved Domains (1) summary
      pfam06003
      Location:27179
      SMN; Survival motor neuron protein (SMN)
    3. XM_011543600.2XP_011541902.1  survival motor neuron protein isoform X3

      See identical proteins and their annotated locations for XP_011541902.1

      UniProtKB/TrEMBL
      B4DP61
      Related
      ENSP00000424282.1, OTTHUMP00000221944, ENST00000511812.5, OTTHUMT00000368718
      Conserved Domains (1) summary
      pfam06003
      Location:27224
      SMN; Survival motor neuron protein (SMN)
    4. XM_011543601.1XP_011541903.1  survival motor neuron protein isoform X4

      See identical proteins and their annotated locations for XP_011541903.1

      Conserved Domains (1) summary
      pfam06003
      Location:27211
      SMN; Survival motor neuron protein (SMN)
    5. XM_011543599.1XP_011541901.1  survival motor neuron protein isoform X1

      See identical proteins and their annotated locations for XP_011541901.1

      UniProtKB/TrEMBL
      E7EQZ4
      Related
      ENSP00000486268.1, ENST00000628696.2
      Conserved Domains (2) summary
      smart00333
      Location:90147
      TUDOR; Tudor domain
      pfam06003
      Location:27278
      SMN; Survival motor neuron protein (SMN)
    6. XM_017009787.1XP_016865276.1  survival motor neuron protein isoform X2

      Related
      ENSP00000492675.1, ENST00000638794.1

    Reference GRCh38.p7 ALT_REF_LOCI_2

    Genomic

    1. NT_187651.1 Reference GRCh38.p7 ALT_REF_LOCI_2

      Range
      274862..302936
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018916.2 Alternate CHM1_1.1

      Range
      69336093..69364167 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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