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SMNDC1 (survival motor neuron domain containing 1)

Identity

Alias_symbol (synonym)SPF30
SMNR
TDRD16C
Other alias
HGNC (Hugo) SMNDC1
LocusID (NCBI) 10285
Atlas_Id 73588
Location 10q25.2  [Link to chromosome band 10q25]
Location_base_pair Starts at 112052798 and ends at 112064707 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
CLCN3 (4q33) / SMNDC1 (10q25.2)LOC100507217 () / SMNDC1 (10q25.2)SMNDC1 (10q25.2) / DAZAP2 (12q13.13)

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)SMNDC1   16900
Cards
Entrez_Gene (NCBI)SMNDC1  10285  survival motor neuron domain containing 1
AliasesSMNR; SPF30; TDRD16C
GeneCards (Weizmann)SMNDC1
Ensembl hg19 (Hinxton) [Gene_View]  chr10:112052798-112064707 [Contig_View]  SMNDC1 [Vega]
Ensembl hg38 (Hinxton) [Gene_View]  chr10:112052798-112064707 [Contig_View]  SMNDC1 [Vega]
TCGA cBioPortalSMNDC1
AceView (NCBI)SMNDC1
Genatlas (Paris)SMNDC1
WikiGenes10285
SOURCE (Princeton)SMNDC1
Genetics Home Reference (NIH)SMNDC1
Genomic and cartography
GoldenPath hg19 (UCSC)SMNDC1  -     chr10:112052798-112064707 -  10q25.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SMNDC1  -     10q25.2   [Description]    (hg38-Dec_2013)
EnsemblSMNDC1 - 10q25.2 [CytoView hg19]  SMNDC1 - 10q25.2 [CytoView hg38]
Mapping of homologs : NCBISMNDC1 [Mapview hg19]  SMNDC1 [Mapview hg38]
OMIM603519   
Gene and transcription
Genbank (Entrez)AF083385 AF107463 AK314013 BC011234 BC039110
RefSeq transcript (Entrez)NM_005871
RefSeq genomic (Entrez)NC_000010 NC_018921 NG_008284 NT_030059 NW_004929376
Consensus coding sequences : CCDS (NCBI)SMNDC1
Cluster EST : UnigeneHs.632093 [ NCBI ]
CGAP (NCI)Hs.632093
Gene ExpressionSMNDC1 [ NCBI-GEO ]   SMNDC1 [ EBI - ARRAY_EXPRESS ]   SMNDC1 [ SEEK ]   SMNDC1 [ MEM ]
Gene Expression Viewer (FireBrowse)SMNDC1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)10285
GTEX Portal (Tissue expression)SMNDC1
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75940   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO75940  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO75940
Splice isoforms : SwissVarO75940
PhosPhoSitePlusO75940
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)SMNDC1
DMDM Disease mutations10285
Blocks (Seattle)SMNDC1
PDB (SRS)4A4F    4A4H   
PDB (PDBSum)4A4F    4A4H   
PDB (IMB)4A4F    4A4H   
PDB (RSDB)4A4F    4A4H   
Structural Biology KnowledgeBase4A4F    4A4H   
SCOP (Structural Classification of Proteins)4A4F    4A4H   
CATH (Classification of proteins structures)4A4F    4A4H   
SuperfamilyO75940
Peptide AtlasO75940
HPRD04627
IPIIPI00025176   
Protein Interaction databases
DIP (DOE-UCLA)O75940
IntAct (EBI)O75940
BioGRIDSMNDC1
STRING (EMBL)SMNDC1
ZODIACSMNDC1
Ontologies - Pathways
QuickGOO75940
Ontology : AmiGOspliceosomal complex assembly  RNA splicing, via transesterification reactions  protein binding  nucleus  nucleoplasm  spliceosomal complex  cytoplasm  mRNA processing  apoptotic process  RNA splicing  Cajal body  nuclear speck  poly(A) RNA binding  intermediate filament cytoskeleton  
Ontology : EGO-EBIspliceosomal complex assembly  RNA splicing, via transesterification reactions  protein binding  nucleus  nucleoplasm  spliceosomal complex  cytoplasm  mRNA processing  apoptotic process  RNA splicing  Cajal body  nuclear speck  poly(A) RNA binding  intermediate filament cytoskeleton  
Pathways : KEGGSpliceosome   
NDEx NetworkSMNDC1
Atlas of Cancer Signalling NetworkSMNDC1
Wikipedia pathwaysSMNDC1
Orthology - Evolution
OrthoDB10285
Phylogenetic Trees/Animal Genes : TreeFamSMNDC1
HOVERGENO75940
HOGENOMO75940
Homologs : HomoloGeneSMNDC1
Homology/Alignments : Family Browser (UCSC)SMNDC1
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMNDC1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMNDC1
dbVarSMNDC1
ClinVarSMNDC1
1000_GenomesSMNDC1 
Exome Variant ServerSMNDC1
ExAC (Exome Aggregation Consortium)SMNDC1 (select the gene name)
Genetic variants : HAPMAP10285
Genomic Variants (DGV)SMNDC1 [DGVbeta]
DECIPHER (Syndromes)10:112052798-112064707  
CONAN: Copy Number AnalysisSMNDC1 
Mutations
ICGC Data PortalSMNDC1 
TCGA Data PortalSMNDC1 
Broad Tumor PortalSMNDC1
OASIS PortalSMNDC1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMNDC1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSMNDC1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SMNDC1
DgiDB (Drug Gene Interaction Database)SMNDC1
DoCM (Curated mutations)SMNDC1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMNDC1 (select a term)
intoGenSMNDC1
Cancer3DSMNDC1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603519   
Orphanet
MedgenSMNDC1
Genetic Testing Registry SMNDC1
NextProtO75940 [Medical]
TSGene10285
GENETestsSMNDC1
Huge Navigator SMNDC1 [HugePedia]
snp3D : Map Gene to Disease10285
BioCentury BCIQSMNDC1
ClinGenSMNDC1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD10285
Chemical/Pharm GKB GenePA134990780
Clinical trialSMNDC1
Miscellaneous
canSAR (ICR)SMNDC1 (select the gene name)
Probes
Litterature
PubMed27 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMNDC1
EVEXSMNDC1
GoPubMedSMNDC1
iHOPSMNDC1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Mar 14 12:44:17 CET 2017

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