SMNDC1 Gene
protein-coding GIFtS: 53
GCID: GC10M112042
|
|
survival motor neuron domain containing 1
| |
Aliases
for SMNDC1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Survival Motor Neuron Domain Containing 11 2 | | 30 KDa Splicing Factor SMNrp2 3 | | SMNR1 2 3 5 | | SMN-Related Protein2 3 | | SPF301 2 3 5 | | Splicing Factor 30, Survival Of Motor Neuron-Related2 | | TDRD16C1 2 | | Survival Of Motor Neuron-Related-Splicing Factor 302 | | Survival Motor Neuron Domain-Containing Protein 12 3 | | Tudor Domain Containing 16C2 |
Export aliases for SMNDC1 gene to outside databasesPrevious GC identifers: GC10M111717 GC10M105683 |
Summaries
for SMNDC1 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for SMNDC1:
This gene is a paralog of SMN1 gene, which encodes the survival motor neuron protein, mutations in which are cause ofautosomal recessive proximal spinal muscular atrophy. The protein encoded by this gene is a nuclear protein that hasbeen identified as a constituent of the spliceosome complex. This gene is differentially expressed, with abundantlevels in skeletal muscle, and may share similar cellular function as the SMN1 gene. (provided by RefSeq, Jul 2008)
UniProtKB/Swiss-Prot: SPF30_HUMAN, O75940Function: Necessary for spliceosome assembly. Overexpression causes apoptosis
Gene Wiki entry for SMNDC1 (Survival motor neuron domain containing 1)
|
Genomic Views
for SMNDC1 gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000010.10 NC_018921.1 NT_030059.13
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the SMNDC1 gene promoter:
HOXA9B HOXA9 ER-alpha MEF-2 Tal-1beta Evi-1 MEF-2A STAT3 aMEF-2
Other transcription factors
Search SABiosciences Chromatin IP Primers for SMNDC1
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SMNDC1 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 10q23 Ensembl cytogenetic band: 10q25.2 HGNC cytogenetic band: 10q23SMNDC1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 10 GeneLoc Exon Structure GeneLoc location for GC10M112042: view genomic region
(about GC identifiers)
Start:
|
112,052,798 bp from pter |
End:
|
112,064,709 bp from pter |
Size:
|
11,912 bases |
Orientation:
|
minus strand |
|
Proteins
for SMNDC1 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: SPF30_HUMAN, O75940 (See
protein sequence)Recommended Name: Survival of motor neuron-related-splicing factor 30 Size: 238 amino acids; 26711 Da
Subunit: Associates with spliceosomes. Associates with U4/U5/U6 tri-snRNP and with U2 snRNP
Subcellular location: Nucleus speckle. Nucleus, Cajal body. Note=Detected in nuclear speckles containing snRNP and inCajal (coiled) bodies
2 PDB 3D structures from  and Proteopedia  for SMNDC1:4A4F (3D)
4A4H (3D)
Secondary accessions: B2RA27 D3DRB1 Q5T3K6Explore the universe of human proteins at neXtProt for SMNDC1: NX_O75940
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_O75940
SMNDC1 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_005862.1
ENSEMBL proteins: ENSP00000358616 ENSP00000358605
Human Recombinant Protein Products:
Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view): About this table
SMNDC1 for ontologies About GeneDecksing
SMNDC1 Antibody Products:
Assay Products for SMNDC1: |
Protein
Domains /
Families
for SMNDC1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
SMNDC1 for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry O75940ProtoNet protein and cluster: O75940 2 Blocks protein families: IPB002999 Tudor domain IPB010304 Survival motor neuron
UniProtKB/Swiss-Prot: SPF30_HUMAN, O75940Domain: The Tudor domain mediates association with dimethylarginines, which are common in snRNP proteinsSimilarity: Belongs to the SMN familySimilarity: Contains 1 Tudor domain |
Function
for SMNDC1 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Function Summary:
UniProtKB/Swiss-Prot: SPF30_HUMAN, O75940Function: Necessary for spliceosome assembly. Overexpression causes apoptosis
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SMNDC1 (see all 2)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMNDC1 |
Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view): About this table
SMNDC1 for ontologies About GeneDecksing
|
Pathways & Interactions
for SMNDC1 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
|
Unified GeneCards pathways About this table
See pathways by source
| Super-pathway | contained gene-specific pathways |
|---|
| 1 | mRNA Splicing - Major Pathway | |
Pathway sources
See GeneCards unified pathways
Show all pathways
1 
Kegg Pathway (Kegg details for SMNDC1):
SMNDC1 for pathways About GeneDecksing
Interactions:
SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SMNDC1
STRING Interaction
Network Preview (showing 5 interactants - click image to see 25)
5/39 Interacting proteins for SMNDC1 (O759401, 2, 3 ENSP000003586054) via UniProtKB, MINT, STRING, and/or I2D (see all 39)About this table
Gene Ontology (GO): 5 biological process terms (GO ID links to tree view): About this table
SMNDC1 for ontologies About GeneDecksing
|
Drugs & Compounds
for SMNDC1 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for SMNDC1
Search CenterWatch for drugs/clinical trials and news about SMNDC1 / SPF30
|
Transcripts
for SMNDC1 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for SMNDC1 gene: NM_005871.3 Unigene Cluster for SMNDC1: Survival motor neuron domain containing 1 Hs.632093 [show with all ESTs]Unigene Representative Sequence: BC0391105 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000369603(uc001kzc.4) ENST00000369592 ENST00000460483 ENST00000471297
ENST00000477763
Clone
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Additional cDNA sequence: AF083385.1 AF107463.1 AK314013.1 BC011234.1 BC039110.1 9 DOTS entries: DT.116225 DT.91643720 DT.100778255 DT.91789763 DT.92430432 DT.95074367 DT.121297735 DT.95349781 DT.97856885 24/190 AceView cDNA sequences (see all 190): AF083385 BM793460 AI702787 BQ067129 BQ024893 AI206293 AI401397 AA504499 AI679475 AW628794 BM352643 CR612539 CF242880 BC039110 AL522559 BU162201 AI306730 NM_005871 BM666320 CB998000 AA338621 AI284362 BE348655 CR591263
GeneLoc Exon Structure
5 Alternative Splicing Database (ASD) splice patterns (SP) for SMNDC1 About this scheme
| ExUns: | 1a | · | 1b | · | 1c | · | 1d | ^ | 2 | ^ | 3 | ^ | 4a | · | 4b | ^ | 5 | ^ | 6a | · | 6b | · | 6c | ^ | 7 |
|---|
|
| SP1: | | | | | | | | | - | | | | - | | - | | | | - | | | | | | | | |
| SP2: | | | | | | | | | - | | | | | | - | | | | - | | | | | | | | |
| SP3: | | | | | | | | | - | | | | - | | - | | | | | | | | | | | | |
| SP4: | | | | | | | | | | | | | - | | - | | | | - | | | | | | | | |
| SP5: | | | | | | | | | - | | | | | | | | | | | | | | | | | |
ECgene alternative splicing isoforms for SMNDC1
|
Expression
for SMNDC1 gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| SMNDC1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
See SMNDC1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for SMNDC1
SOURCE GeneReport for Unigene cluster: Hs.632093
UniProtKB/Swiss-Prot: SPF30_HUMAN, O75940Tissue specificity: Detected at intermediate levels in skeletal muscle, and at low levels in heart and pancreas
SABiosciences Expression via Pathway-Focused PCR Array including SMNDC1:
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for SMNDC1
Browse OriGene validated miRNA SYBR primer pairs
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Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMNDC1 |
Orthologs
for SMNDC1 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the common ancestor of eukaryotes.
Orthologs for SMNDC1 gene from 9/29 species (see all 29) About this table
| Organism |
Taxonomic
classification |
Gene |
Description |
Human
Similarity |
Orthology
Type |
Details |
mouse
(Mus musculus) |
Mammalia |
Smndc11 , 5 |
survival motor neuron domain containing 11, 5 |
90.06(n)1
99.58(a)1 |
|
19 (47.67 cM)5
764791 NM_172429.21 NP_766017.11
533792145 |
chicken
(Gallus gallus) |
Aves |
SMNDC11 |
survival motor neuron domain containing 1 |
85.29(n)
95.8(a) |
|
423889 XM_421753.3 XP_421753.2 |
lizard
(Anolis carolinensis) |
Reptilia |
SMNDC16 |
-- |
95(a) |
1 ↔ 1 |
3(45172755-45180702) |
African clawed frog
(Xenopus laevis) |
Amphibia |
LOC3979002 |
X.laevis histone H1-like maternal (B4) protein mRNA, more |
79.87(n) |
|
M36655.1 |
zebrafish
(Danio rerio) |
Actinopterygii |
BC045967.12 |
-- |
75.31(n) |
|
BC045967.1 |
fruit fly
(Drosophila melanogaster) |
Insecta |
CG174541 |
CG17454 |
51.23(n)
49.54(a) |
|
7354399 NM_001144529.1 NP_001138001.1 |
worm
(Caenorhabditis elegans) |
Secernentea |
smr-11 |
Protein SMR-1 |
44.33(n)
39.18(a) |
|
175281 NM_001027761.3 NP_001022932.1 |
thale cress
(Arabidopsis thaliana) |
eudicotyledons |
AT2G025706 |
survival of motor neuron-related-splicing factor 3... |
23(a) |
1 ↔ 1 |
2(697951-700917) |
rice
(Oryza sativa) |
Liliopsida |
-- |
nucleic acid binding protein, putative, expressed |
26(a) |
1 ↔ 1 |
8(512747-517277) |
ENSEMBL Gene Tree for SMNDC1 (if available)
TreeFam Gene Tree for SMNDC1 (if available) |
Paralogs
for SMNDC1 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for SMNDC1 gene
- SMN12 SMN22
SMNDC1 for paralogs About GeneDecksing
1 Pseudogenes.org Pseudogene for SMNDC1
PGOHUM00000247520
|
Genomic Variants
for SMNDC1 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 10 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for SMNDC1 (112052798 - 112064709 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for SMNDC1: -- | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SMNDC1 |
|
Disorders
/ Diseases
for SMNDC1 gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
SMNDC1 for disorders About GeneDecksing
OMIM gene information: 603519
OMIM disorders: --
7  diseases for SMNDC1: About MalaCardsspinal muscular atrophy proximal spinal muscular atrophy muscular atrophy neuronitis
rosacea skin cancer alzheimer's disease
Human Genome Epidemiology (HuGE) Navigator: SMNDC1 (1 document)
Export disorders for SMNDC1 gene to outside databases
|
Publications
for SMNDC1 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
|
PubMed articles for SMNDC1 gene, integrated from 9 sources (see all 30):
(articles sorted by number of sources associating them with SMNDC1) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. (PubMed id 9731529)1, 2, 3 Neubauer G.... Mann M. (1998)
- Characterization of a gene encoding survival motor neuron (SMN)- related protein, a constituent of the spliceosome complex. (PubMed id 9817934)1, 2, 3 Talbot K.... Davies K.E. (1998)
- Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. (PubMed id 22101937)1, 2 Tripsianes K.... Sattler M. (2011)
- A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (2006)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
- SMNrp is an essential pre-mRNA splicing factor required for the formation of the mature spliceosome. (PubMed id 11331595)1, 2 Meister G.... Fischer U. (2001)
- SPF30 is an essential human splicing factor required for assembly of the U4/U5/U6 tri-small nuclear ribonucleoprotein into the spliceosome. (PubMed id 11331295)1, 2 Rappsilber J.... Mann M. (2001)
- Splicing factor SPF30 bridges an interaction between the prespliceosome protein U2AF35 and tri-small nuclear ribonucleoprotein protein hPrp3. (PubMed id 18211889)1, 9 Little J.T. and Jurica M.S. (2008)
- A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
- Crystal structure of TDRD3 and methyl-arginine binding characterization of TDRD3, SMN and SPF30. (PubMed id 22363433)1 Liu K....Min J. (2012)
|
External Searches for SMNDC1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing SMNDC1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing SMNDC1 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing SMNDC1 gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for SMNDC1 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for SMNDC1 gene:
Search GeneIP for patents involving SMNDC1
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for SMNDC1 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section
|
 | |
 | |
 |
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| |
 |
 |
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| |
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| |  |  |  |  | | | | | | Recombinant Protein for SMNDC1 |
|
 |
 |
 |
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| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMNDC1 |
|  |  |  | | | | ThermoFisher Antibodies for SMNDC1 |
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