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

Gene ID: 6607, updated on 10-Jul-2014
Official Symbol
SMN2provided by HGNC
Official Full Name
survival of motor neuron 2, centromericprovided by HGNC
Primary source
HGNC:11118
See related
Ensembl:ENSG00000205571; HPRD:09036; 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]
See SMN2 in Epigenomics, MapViewer
Location:
5q13.2
Exon count :
9
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 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 LOC102724356 Neighboring gene cadherin 12 (N-cadherin 2) pseudogene 2 Neighboring gene small EDRK-rich factor 1B (centromeric) Neighboring gene NLR family, apoptosis inhibitory protein pseudogene Neighboring gene cadherin 12 (N-cadherin 2) pseudogene 3 Neighboring gene glucuronidase, beta pseudogene

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

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
RNA metabolic process TAS
Traceable Author Statement
more info
 
cell death IEA
Inferred from Electronic Annotation
more info
 
gene expression TAS
Traceable Author Statement
more info
 
ncRNA metabolic process TAS
Traceable Author Statement
more info
 
nervous system development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein import into nucleus IDA
Inferred from Direct Assay
more info
PubMed 
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 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
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 
Preferred Names
survival motor neuron protein
Names
survival motor neuron protein
gemin-1
component of gems 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 

    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 proteins identical to 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, OTTHUMP00000125236, ENST00000380743, OTTHUMT00000216845
    Conserved Domains (2) summary
    pfam06003
    Location:26291
    Blast Score: 704
    SMN; Survival motor neuron protein (SMN)
    cd04508
    Location:95141
    Blast Score: 143
    TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
  2. NM_022875.2NP_075013.1  survival motor neuron protein isoform a

    See proteins identical to 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
    ENSP00000370117, ENST00000380741
    Conserved Domains (2) summary
    pfam06003
    Location:26278
    Blast Score: 678
    SMN; Survival motor neuron protein (SMN)
    cd04508
    Location:95141
    Blast Score: 143
    TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
  3. NM_022876.2NP_075014.1  survival motor neuron protein isoform b

    See proteins identical to 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, OTTHUMP00000125237, ENST00000380742, OTTHUMT00000216846
    Conserved Domains (2) summary
    pfam06003
    Location:26259
    Blast Score: 674
    SMN; Survival motor neuron protein (SMN)
    cd04508
    Location:95141
    Blast Score: 143
    TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
  4. NM_022877.2NP_075015.1  survival motor neuron protein isoform c

    See proteins identical to 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
    pfam06003
    Location:26246
    Blast Score: 648
    SMN; Survival motor neuron protein (SMN)
    cd04508
    Location:95141
    Blast Score: 143
    TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 ALT_REF_LOCI_2

Genomic

  1. NT_187651.1 

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000005.10 

    Range
    70049523..70077595
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. NW_001841229.1 

    Range
    81..6003
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018916.2 

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

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