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SMN1 (survival of motor neuron 1, telomeric)

Identity

Alias_namesSMA@
SMA
spinal muscular atrophy (Werdnig-Hoffmann disease
Alias_symbol (synonym)BCD541
SMNT
SMA1
SMA2
SMA3
GEMIN1
TDRD16A
Other aliasSMA4
SMN
T-BCD541
HGNC (Hugo) SMN1
LocusID (NCBI) 6606
Atlas_Id 54929
Location 5q13.2  [Link to chromosome band 5q13]
Location_base_pair Starts at 70049523 and ends at 70077591 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)SMN1   11117
LRG (Locus Reference Genomic)LRG_676
Cards
Entrez_Gene (NCBI)SMN1  6606  survival of motor neuron 1, telomeric
AliasesBCD541; GEMIN1; SMA; SMA1; 
SMA2; SMA3; SMA4; SMA@; SMN; SMNT; T-BCD541; TDRD16A
GeneCards (Weizmann)SMN1
Ensembl hg19 (Hinxton)ENSG00000172062 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000172062 [Gene_View]  chr5:70049523-70077591 [Contig_View]  SMN1 [Vega]
ICGC DataPortalENSG00000172062
TCGA cBioPortalSMN1
AceView (NCBI)SMN1
Genatlas (Paris)SMN1
WikiGenes6606
SOURCE (Princeton)SMN1
Genetics Home Reference (NIH)SMN1
Genomic and cartography
GoldenPath hg38 (UCSC)SMN1  -     chr5:70049523-70077591 +  5q13.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMN1  -     5q13.2   [Description]    (hg19-Feb_2009)
EnsemblSMN1 - 5q13.2 [CytoView hg19]  SMN1 - 5q13.2 [CytoView hg38]
Mapping of homologs : NCBISMN1 [Mapview hg19]  SMN1 [Mapview hg38]
OMIM253300   253400   253550   271150   600354   
Gene and transcription
Genbank (Entrez)AK298203 BC062723 DQ894095 EU176224 JQ657798
RefSeq transcript (Entrez)NM_000344 NM_001297715 NM_022874
RefSeq genomic (Entrez)NC_000005 NC_018916 NG_008691 NT_187651 NW_003315917
Consensus coding sequences : CCDS (NCBI)SMN1
Cluster EST : UnigeneHs.535788 [ NCBI ]
CGAP (NCI)Hs.535788
Alternative Splicing GalleryENSG00000172062
Gene ExpressionSMN1 [ NCBI-GEO ]   SMN1 [ EBI - ARRAY_EXPRESS ]   SMN1 [ SEEK ]   SMN1 [ MEM ]
Gene Expression Viewer (FireBrowse)SMN1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6606
GTEX Portal (Tissue expression)SMN1
Human Protein AtlasENSG00000172062-SMN1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ16637   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ16637  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ16637
Splice isoforms : SwissVarQ16637
PhosPhoSitePlusQ16637
Domaine pattern : Prosite (Expaxy)TUDOR (PS50304)   
Domains : Interpro (EBI)Survival_motor_neuron    Tudor   
Domain families : Pfam (Sanger)SMN (PF06003)   
Domain families : Pfam (NCBI)pfam06003   
Domain families : Smart (EMBL)TUDOR (SM00333)  
Conserved Domain (NCBI)SMN1
DMDM Disease mutations6606
Blocks (Seattle)SMN1
PDB (SRS)1G5V    1MHN    2LEH    3S6N    4A4E    4A4G    4GLI    4QQ6   
PDB (PDBSum)1G5V    1MHN    2LEH    3S6N    4A4E    4A4G    4GLI    4QQ6   
PDB (IMB)1G5V    1MHN    2LEH    3S6N    4A4E    4A4G    4GLI    4QQ6   
PDB (RSDB)1G5V    1MHN    2LEH    3S6N    4A4E    4A4G    4GLI    4QQ6   
Structural Biology KnowledgeBase1G5V    1MHN    2LEH    3S6N    4A4E    4A4G    4GLI    4QQ6   
SCOP (Structural Classification of Proteins)1G5V    1MHN    2LEH    3S6N    4A4E    4A4G    4GLI    4QQ6   
CATH (Classification of proteins structures)1G5V    1MHN    2LEH    3S6N    4A4E    4A4G    4GLI    4QQ6   
SuperfamilyQ16637
Human Protein Atlas [tissue]ENSG00000172062-SMN1 [tissue]
Peptide AtlasQ16637
HPRD02646
IPIIPI00003394   IPI00219360   IPI00009597   IPI00009598   IPI00966114   IPI00981303   
Protein Interaction databases
DIP (DOE-UCLA)Q16637
IntAct (EBI)Q16637
FunCoupENSG00000172062
BioGRIDSMN1
STRING (EMBL)SMN1
ZODIACSMN1
Ontologies - Pathways
QuickGOQ16637
Ontology : AmiGOspliceosomal complex assembly  spliceosomal complex assembly  spliceosomal snRNP assembly  spliceosomal snRNP assembly  RNA binding  protein binding  nucleus  nucleoplasm  nucleoplasm  cytoplasm  cytosol  cytosol  DNA-templated transcription, termination  nervous system development  Cajal body  Z disc  SMN complex  SMN-Sm protein complex  cytoplasmic ribonucleoprotein granule  identical protein binding  neuron projection  perikaryon  nuclear import  Gemini of coiled bodies  
Ontology : EGO-EBIspliceosomal complex assembly  spliceosomal complex assembly  spliceosomal snRNP assembly  spliceosomal snRNP assembly  RNA binding  protein binding  nucleus  nucleoplasm  nucleoplasm  cytoplasm  cytosol  cytosol  DNA-templated transcription, termination  nervous system development  Cajal body  Z disc  SMN complex  SMN-Sm protein complex  cytoplasmic ribonucleoprotein granule  identical protein binding  neuron projection  perikaryon  nuclear import  Gemini of coiled bodies  
Pathways : KEGGRNA transport   
NDEx NetworkSMN1
Atlas of Cancer Signalling NetworkSMN1
Wikipedia pathwaysSMN1
Orthology - Evolution
OrthoDB6606
GeneTree (enSembl)ENSG00000172062
Phylogenetic Trees/Animal Genes : TreeFamSMN1
HOVERGENQ16637
HOGENOMQ16637
Homologs : HomoloGeneSMN1
Homology/Alignments : Family Browser (UCSC)SMN1
Gene fusions - Rearrangements
Tumor Fusion PortalSMN1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMN1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMN1
dbVarSMN1
ClinVarSMN1
1000_GenomesSMN1 
Exome Variant ServerSMN1
ExAC (Exome Aggregation Consortium)ENSG00000172062
GNOMAD BrowserENSG00000172062
Genetic variants : HAPMAP6606
Genomic Variants (DGV)SMN1 [DGVbeta]
DECIPHERSMN1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMN1 
Mutations
ICGC Data PortalSMN1 
TCGA Data PortalSMN1 
Broad Tumor PortalSMN1
OASIS PortalSMN1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMN1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSMN1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)Leiden Muscular Dystrophy pages
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SMN1
DgiDB (Drug Gene Interaction Database)SMN1
DoCM (Curated mutations)SMN1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMN1 (select a term)
intoGenSMN1
Cancer3DSMN1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM253300    253400    253550    271150    600354   
Orphanet11563    11566    11567    11565   
DisGeNETSMN1
MedgenSMN1
Genetic Testing Registry SMN1
NextProtQ16637 [Medical]
TSGene6606
GENETestsSMN1
Target ValidationSMN1
Huge Navigator SMN1 [HugePedia]
snp3D : Map Gene to Disease6606
BioCentury BCIQSMN1
ClinGenSMN1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6606
Chemical/Pharm GKB GenePA35966
Clinical trialSMN1
Miscellaneous
canSAR (ICR)SMN1 (select the gene name)
Probes
Litterature
PubMed288 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMN1
EVEXSMN1
GoPubMedSMN1
iHOPSMN1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 14:35:39 CET 2017

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