InnateDB: Systems Biology of the Innate Immune Response

Homo sapiens Gene: SMN2

Summary

InnateDB Gene

IDBG-26417.6

Last Modified

2014-10-13 [Report errors or provide feedback]

Gene Symbol

SMN2

Gene Name

survival of motor neuron 2, centromeric

Synonyms

Species

Homo sapiens

Ensembl Gene

ENSG00000205571

Encoded Proteins

IDBP-26419

survival of motor neuron 2, centromeric

IDBP-26421

survival of motor neuron 2, centromeric

IDBP-26423

survival of motor neuron 2, centromeric

IDBP-484435

survival of motor neuron 2, centromeric

IDBP-485326

survival of motor neuron 2, centromeric

IDBP-810174

survival of motor neuron 2, centromeric

IDBP-810178

survival of motor neuron 2, centromeric

IDBP-810179

survival of motor neuron 2, centromeric

Protein Structure

Useful resources

Stemformatics EHFPI ImmGen

Entrez Gene

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] 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]

Gene Information

Type

Protein coding

Genomic Location

Chromosome 5:70049612-70078522

Strand

Forward strand

Band

q13.2

Transcripts

ENST00000380743	ENSP00000370119
ENST00000380742	ENSP00000370118
ENST00000380741	ENSP00000370117
ENST00000511812	ENSP00000424282
ENST00000506734	ENSP00000424799
ENST00000503678
ENST00000511873	ENSP00000475824
ENST00000509805
ENST00000505346
ENST00000514914
ENST00000508258
ENST00000507458	ENSP00000475331
ENST00000614240	ENSP00000479279

Interactions

Number of Interactions

This gene and/or its encoded proteins are associated with 20 experimentally validated interaction(s) in this database.

Experimentally validated
Total	20 [view]
Protein-Protein	20 [view]
Protein-DNA	0
Protein-RNA	0
DNA-DNA	0
RNA-RNA	0
DNA-RNA	0

Gene Ontology

Molecular Function

Accession	GO Term
GO:0003723	RNA binding
GO:0005515	protein binding
GO:0042802	identical protein binding

Biological Process

GO:0000245	spliceosomal complex assembly
GO:0000387	spliceosomal snRNP assembly
GO:0006397	mRNA processing
GO:0007399	nervous system development
GO:0008219	cell death
GO:0010467	gene expression
GO:0016070	RNA metabolic process
GO:0034660	ncRNA metabolic process
GO:0042307	positive regulation of protein import into nucleus

Cellular Component

GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0015030	Cajal body
GO:0030018	Z disc
GO:0032797	SMN complex
GO:0034719	SMN-Sm protein complex
GO:0097504	Gemini of coiled bodies

Orthologs

No orthologs found for this gene

Pathways

NETPATH

REACTOME

REACT_11066

snRNP Assembly pathway

REACT_11052

Metabolism of non-coding RNA pathway

REACT_71

Gene Expression pathway

KEGG

hsa03013

RNA transport pathway

INOH

PID NCI

Cross-References

SwissProt

TrEMBL

UniProt Splice Variant

Entrez Gene

UniGene

Hs.202179

RefSeq

NM_017411 NM_022875 NM_022876

HUGO

OMIM

CCDS

CCDS4007 CCDS4008

HPRD

09036

IMGT

EMBL

GenPept

RNA Seq Atlas