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

Gene ID: 6606, updated on 9-Jul-2014
Official Symbol
SMN1provided by HGNC
Official Full Name
survival of motor neuron 1, telomericprovided by HGNC
Primary source
HGNC:11117
See related
Ensembl:ENSG00000172062; HPRD:02646; 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]
See SMN1 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 (70924941..70953012)
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 uncharacterized LOC102724275 Neighboring gene cadherin 12 (N-cadherin 2) pseudogene 1 Neighboring gene small EDRK-rich factor 1A (telomeric) Neighboring gene NLR family, apoptosis inhibitory protein Neighboring gene general transcription factor IIH, polypeptide 2, 44kDa

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Protein interactions

Protein Gene Interaction Pubs
Tat, p14 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
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 Protein 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

Preferred Names
survival motor neuron protein
Names
survival motor neuron protein
gemin-1
component of gems 1
tudor domain containing 16A
survival motor neuron 1 protein

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 

    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 proteins identical to 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, OTTHUMP00000125198, ENST00000380707, OTTHUMT00000216805
    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_022874.2NP_075012.1  survival motor neuron protein isoform b

    See proteins identical to 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
    ENSP00000305857, ENST00000351205
    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 ...

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_1

Genomic

  1. NW_003315917.2 

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

mRNA and Protein(s)

  1. XM_005276775.1XP_005276832.1  

    See proteins identical to XP_005276832.1

    UniProtKB/Swiss-Prot
    Q16637
    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 ...

Reference GRCh38 ALT_REF_LOCI_2

Genomic

  1. NT_187651.1 

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

mRNA and Protein(s)

  1. XM_005248575.2XP_005248632.1  

    See proteins identical to XP_005248632.1

    UniProtKB/Swiss-Prot
    Q16637
    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 ...

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000005.10 

    Range
    70924941..70953012
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006714677.1XP_006714740.1  

    See proteins identical to XP_006714740.1

    UniProtKB/Swiss-Prot
    Q16637
    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 ...

Alternate HuRef

Genomic

  1. AC_000137.1 

    Range
    65881629..65882701
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018916.2 

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

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