This gene is a paralog of SMN1 gene, which encodes the survival motor neuron protein, mutations in which are cause of autosomal recessive proximal spinal muscular atrophy. The protein encoded by this gene is a nuclear protein that has been identified as a constituent of the spliceosome complex. This gene is differentially expressed, with abundant levels in skeletal muscle, and ... See more...

Aliases for SMNDC1 Gene

Aliases for SMNDC1 Gene

  • Survival Motor Neuron Domain Containing 1 2 3 5
  • SPF30 2 3 4
  • SMNR 2 3 4
  • Splicing Factor 30, Survival Of Motor Neuron-Related 2 3
  • Survival Of Motor Neuron-Related-Splicing Factor 30 3 4
  • Survival Motor Neuron Domain-Containing Protein 1 3 4
  • 30 KDa Splicing Factor SMNrp 3 4
  • Tudor Domain Containing 16C 2 3
  • SMN-Related Protein 3 4
  • TDRD16C 2 3
  • SMNDC1 5

External Ids for SMNDC1 Gene

Previous GeneCards Identifiers for SMNDC1 Gene

  • GC10M111717
  • GC10M112042
  • GC10M105683

Summaries for SMNDC1 Gene

Entrez Gene Summary for SMNDC1 Gene

  • This gene is a paralog of SMN1 gene, which encodes the survival motor neuron protein, mutations in which are cause of autosomal recessive proximal spinal muscular atrophy. The protein encoded by this gene is a nuclear protein that has been identified as a constituent of the spliceosome complex. This gene is differentially expressed, with abundant levels in skeletal muscle, and may share similar cellular function as the SMN1 gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for SMNDC1 Gene

SMNDC1 (Survival Motor Neuron Domain Containing 1) is a Protein Coding gene. Diseases associated with SMNDC1 include Spinal Muscular Atrophy and Proximal Spinal Muscular Atrophy. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway. Gene Ontology (GO) annotations related to this gene include RNA binding. An important paralog of this gene is SMN2.

UniProtKB/Swiss-Prot Summary for SMNDC1 Gene

Gene Wiki entry for SMNDC1 Gene

Additional gene information for SMNDC1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SMNDC1 Gene

Genomics for SMNDC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SMNDC1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J110303 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 +0.0 23 3.5 BRCA1 ARHGAP35 SP1 CREB1 CTCF TEAD4 PRDM10 REST ZNF629 IKZF1 SMNDC1 lnc-XPNPEP1-4 MXI1
GH10J110566 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 24.2 -263.3 -263295 4.5 BRCA1 SP1 GATAD2A ATF7 TEAD4 PRDM10 TFE3 SOX13 IKZF1 NFKBIZ SMC3 LOC105378483 SMNDC1 XPNPEP1 ENSG00000270589 RBM20 SNODB1234
GH10J110915 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 20.2 -614.4 -614359 6.9 SP1 CREB1 PRDM10 ZNF629 REST RFX1 SIX5 LEF1 IKZF1 KDM1A BBIP1 SHOC2 lnc-SMNDC1-8 SMC3 SMNDC1 XPNPEP1 ADRA2A PDCD4 ENSG00000270589
GH10J110206 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 14.3 +94.9 94872 6.6 BRCA1 ARHGAP35 SP1 HNRNPL CREB1 GATAD2A ATF7 PRDM10 ZNF629 TFE3 MXI1 ENSG00000228417 SMNDC1 ADD3 lnc-SMNDC1-9
GH10J110220 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.9 +82.9 82944 2.8 CREB1 CTCF ATF7 PRDM10 ZNF629 RFX1 LEF1 IKZF1 RFX5 ZNF692 MXI1 lnc-SMNDC1-9 SMNDC1 BBIP1 ADD3 LOC105378480
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMNDC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SMNDC1

Top Transcription factor binding sites by QIAGEN in the SMNDC1 gene promoter:
  • aMEF-2
  • ER-alpha
  • Evi-1
  • HOXA9
  • HOXA9B
  • MEF-2
  • MEF-2A
  • STAT3
  • Tal-1beta

Genomic Locations for SMNDC1 Gene

Genomic Locations for SMNDC1 Gene
chr10:110,290,730-110,304,969
(GRCh38/hg38)
Size:
14,240 bases
Orientation:
Minus strand
chr10:112,050,488-112,064,709
(GRCh37/hg19)
Size:
14,222 bases
Orientation:
Minus strand

Genomic View for SMNDC1 Gene

Genes around SMNDC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMNDC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMNDC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMNDC1 Gene

Proteins for SMNDC1 Gene

  • Protein details for SMNDC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75940-SPF30_HUMAN
    Recommended name:
    Survival of motor neuron-related-splicing factor 30
    Protein Accession:
    O75940
    Secondary Accessions:
    • B2RA27
    • D3DRB1
    • Q5T3K6

    Protein attributes for SMNDC1 Gene

    Size:
    238 amino acids
    Molecular mass:
    26711 Da
    Quaternary structure:
    • Associates with spliceosomes. Associates with U4/U5/U6 tri-snRNP and with U2 snRNP.

    Three dimensional structures from OCA and Proteopedia for SMNDC1 Gene

neXtProt entry for SMNDC1 Gene

Post-translational modifications for SMNDC1 Gene

  • Ubiquitination at Lys165
  • Modification sites at PhosphoSitePlus

Other Protein References for SMNDC1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SMNDC1 Gene

Domains & Families for SMNDC1 Gene

Gene Families for SMNDC1 Gene

Protein Domains for SMNDC1 Gene

InterPro:
Blocks:
  • Tudor domain
  • Survival motor neuron
ProtoNet:

Suggested Antigen Peptide Sequences for SMNDC1 Gene

GenScript: Design optimal peptide antigens:
  • Survival motor neuron domain-containing protein 1 (SPF30_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O75940

UniProtKB/Swiss-Prot:

SPF30_HUMAN :
  • The Tudor domain mediates association with dimethylarginines, which are common in snRNP proteins.
  • Belongs to the SMN family.
Domain:
  • The Tudor domain mediates association with dimethylarginines, which are common in snRNP proteins.
Family:
  • Belongs to the SMN family.
genes like me logo Genes that share domains with SMNDC1: view

Function for SMNDC1 Gene

Molecular function for SMNDC1 Gene

UniProtKB/Swiss-Prot Function:
Necessary for spliceosome assembly. Overexpression causes apoptosis.

Phenotypes From GWAS Catalog for SMNDC1 Gene

Gene Ontology (GO) - Molecular Function for SMNDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 15494309
genes like me logo Genes that share ontologies with SMNDC1: view
genes like me logo Genes that share phenotypes with SMNDC1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMNDC1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SMNDC1 Gene

Localization for SMNDC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMNDC1 Gene

Nucleus speckle. Nucleus, Cajal body. Note=Detected in nuclear speckles containing snRNP and in Cajal (coiled) bodies.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMNDC1 gene
Compartment Confidence
nucleus 5
cytoskeleton 3
cytosol 3
extracellular 2
plasma membrane 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
  • Nuclear bodies (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SMNDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 9817934
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005737 cytoplasm IEA --
GO:0015030 Cajal body IEA --
genes like me logo Genes that share ontologies with SMNDC1: view

Pathways & Interactions for SMNDC1 Gene

genes like me logo Genes that share pathways with SMNDC1: view

Pathways by source for SMNDC1 Gene

Gene Ontology (GO) - Biological Process for SMNDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000375 RNA splicing, via transesterification reactions TAS 9731529
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0006915 apoptotic process TAS,IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with SMNDC1: view

No data available for SIGNOR curated interactions for SMNDC1 Gene

Drugs & Compounds for SMNDC1 Gene

No Compound Related Data Available

Transcripts for SMNDC1 Gene

mRNA/cDNA for SMNDC1 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMNDC1

Alternative Splicing Database (ASD) splice patterns (SP) for SMNDC1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7
SP1: - - - -
SP2: - - -
SP3: - - -
SP4: - - -
SP5: -

Relevant External Links for SMNDC1 Gene

GeneLoc Exon Structure for
SMNDC1

Expression for SMNDC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SMNDC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SMNDC1 Gene

This gene is overexpressed in Breast (26.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SMNDC1 Gene



Protein tissue co-expression partners for SMNDC1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SMNDC1

SOURCE GeneReport for Unigene cluster for SMNDC1 Gene:

Hs.632093

mRNA Expression by UniProt/SwissProt for SMNDC1 Gene:

O75940-SPF30_HUMAN
Tissue specificity: Detected at intermediate levels in skeletal muscle, and at low levels in heart and pancreas.

Evidence on tissue expression from TISSUES for SMNDC1 Gene

  • Nervous system(4.6)
  • Muscle(2.8)
  • Heart(2.7)
  • Skin(2.7)
  • Lung(2.6)
  • Kidney(2.6)
  • Spleen(2.6)
  • Liver(2.4)
  • Intestine(2.4)
  • Blood(2.3)
  • Bone marrow(2.2)
  • Lymph node(2.1)
genes like me logo Genes that share expression patterns with SMNDC1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMNDC1 Gene

Orthologs for SMNDC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SMNDC1 Gene

Organism Taxonomy Gene Similarity Type Details
Oppossum
(Monodelphis domestica)
Mammalia SMNDC1 31
  • 100 (a)
OneToOne
Chimpanzee
(Pan troglodytes)
Mammalia SMNDC1 30 31
  • 99.86 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SMNDC1 31
  • 98 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SMNDC1 30 31
  • 95.8 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SMNDC1 30 31
  • 94.68 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Smndc1 30 17 31
  • 90.06 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Smndc1 30
  • 90.06 (n)
Chicken
(Gallus gallus)
Aves SMNDC1 30 31
  • 85.29 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SMNDC1 31
  • 95 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia smndc1 30
  • 76.05 (n)
African clawed frog
(Xenopus laevis)
Amphibia LOC397900 30
Zebrafish
(Danio rerio)
Actinopterygii smndc1 30 31
  • 69.2 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7875 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006247 30
  • 52.6 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG17454 30 31
  • 51.08 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea smr-1 31
  • 31 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.10154 31
  • 47 (a)
OneToOne
Species where no ortholog for SMNDC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SMNDC1 Gene

ENSEMBL:
Gene Tree for SMNDC1 (if available)
TreeFam:
Gene Tree for SMNDC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SMNDC1: view image

Paralogs for SMNDC1 Gene

Paralogs for SMNDC1 Gene

Pseudogenes.org Pseudogenes for SMNDC1 Gene

genes like me logo Genes that share paralogs with SMNDC1: view

Variants for SMNDC1 Gene

Additional dbSNP identifiers (rs#s) for SMNDC1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SMNDC1 Gene

Variant ID Type Subtype PubMed ID
nsv7211 OTHER inversion 18451855

Variation tolerance for SMNDC1 Gene

Residual Variation Intolerance Score: 45.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.47; 10.21% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMNDC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMNDC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SMNDC1 Gene

Disorders for SMNDC1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for SMNDC1 Gene - From: GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
spinal muscular atrophy
  • progressive muscular atrophy
proximal spinal muscular atrophy
  • sma
muscular atrophy
  • amyotrophia
ophthalmia nodosa
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SMNDC1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SMNDC1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SMNDC1 Gene

Publications for SMNDC1 Gene

  1. Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. (PMID: 9731529) Neubauer G … Mann M (Nature genetics 1998) 2 3 4
  2. Characterization of a gene encoding survival motor neuron (SMN)-related protein, a constituent of the spliceosome complex. (PMID: 9817934) Talbot K … Davies KE (Human molecular genetics 1998) 2 3 4
  3. Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. (PMID: 22101937) Tripsianes K … Sattler M (Nature structural & molecular biology 2011) 3 4
  4. Splicing factor SPF30 bridges an interaction between the prespliceosome protein U2AF35 and tri-small nuclear ribonucleoprotein protein hPrp3. (PMID: 18211889) Little JT … Jurica MS (The Journal of biological chemistry 2008) 3 23
  5. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PMID: 16964243) Beausoleil SA … Gygi SP (Nature biotechnology 2006) 3 4

Products for SMNDC1 Gene

  • Signalway Proteins for SMNDC1

Sources for SMNDC1 Gene