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Aliases for SMNDC1 Gene

Aliases for SMNDC1 Gene

  • Survival Motor Neuron Domain Containing 1 2 3 5
  • Splicing Factor 30, Survival Of Motor Neuron-Related 2 3
  • 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
  • SPF30 3 4
  • SMNR 3 4
  • Survival Of Motor Neuron-Related-Splicing Factor 30 3
  • TDRD16C 3

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 Muscular Atrophy and Spinal Muscular Atrophy. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. GO annotations related to this gene include poly(A) RNA binding and RNA binding.

UniProtKB/Swiss-Prot for SMNDC1 Gene

  • Necessary for spliceosome assembly. Overexpression causes apoptosis.

Gene Wiki entry for SMNDC1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMNDC1 Gene

Genomics for SMNDC1 Gene

Regulatory Elements for SMNDC1 Gene

Enhancers for SMNDC1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10F110930 0.4 Ensembl 36.3 -627.0 -626950 2.2 ZNF493 ZFP64 ZNF121 ZNF354C FOS ZNF202 ZNF680 ZNF654 ZBTB11 REST SMC3 SMNDC1 ENSG00000270589 ADRA2A BBIP1 MIR4680 PDCD4 ENSG00000232470 RPL13AP6 SHOC2
GH10F110406 1.1 FANTOM5 Ensembl ENCODE 23.6 -107.5 -107477 11.2 HDGF PKNOX1 WRNIP1 ARID4B SIN3A YBX1 ZNF48 BRCA1 YY1 ELK1 SMNDC1 DUSP5 SMC3 PDCD4-AS1 HMGB3P5 GC10P110318
GH10F110651 1 Ensembl ENCODE 15.4 -346.7 -346654 0.9 FEZF1 UBTF ZBTB40 FOXK2 ZBTB48 FOS ZNF548 ZNF600 CREM ZNF263 SMNDC1 SMC3 RBM20 GC10P110732
GH10F111076 0.7 ENCODE 15.4 -772.2 -772240 2.0 INSM2 KLF17 ZNF2 RAD21 ZEB1 YY1 GLIS2 ZNF366 ZNF143 ZNF548 SMC3 RPL7P35 SMNDC1 BBIP1 ADRA2A GC10P111079 PIR36818
GH10F110136 0.9 Ensembl ENCODE 14.6 +167.2 167220 2.1 ELF3 HDGF PKNOX1 ARID4B ZNF2 RAD21 ZEB1 RFX5 YY1 ZNF143 SMC3 SMNDC1 SNRPGP12 GC10M110015 GC10M110016
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SMNDC1 on UCSC Golden Path with GeneCards custom track

Promoters for SMNDC1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000006844 251 2601 ATF1 PKNOX1 CREB3L1 ARID4B SIN3A FEZF1 DMAP1 ZNF48 BRCA1 YY1

Genomic Location for SMNDC1 Gene

Chromosome:
10
Start:
110,290,730 bp from pter
End:
110,304,951 bp from pter
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 Lys 165
  • 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

Suggested Antigen Peptide Sequences for SMNDC1 Gene

GenScript: Design optimal peptide antigens:

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.
  • Contains 1 Tudor domain.
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.

Gene Ontology (GO) - Molecular Function for SMNDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 15494309
GO:0044822 poly(A) RNA binding IDA 22658674
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

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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
Jensen Localization Image for SMNDC1 Gene COMPARTMENTS Subcellular localization image for SMNDC1 gene
Compartment Confidence
nucleus 5
cytosol 3
cytoskeleton 2

Gene Ontology (GO) - Cellular Components for SMNDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,TAS 9817934
GO:0005681 spliceosomal complex IEA --
GO:0005737 cytoplasm IEA --
GO:0015030 Cajal body IEA --
GO:0016607 nuclear speck 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:0006397 mRNA processing IEA --
GO:0006915 apoptotic process 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

Transcripts for SMNDC1 Gene

Unigene Clusters for SMNDC1 Gene

Survival motor neuron domain containing 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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
ECgene alternative splicing isoforms 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, PaxDb, MaxQB, and MOPED for SMNDC1 Gene



Protein tissue co-expression partners for SMNDC1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SMNDC1 Gene:

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.
genes like me logo Genes that share expression patterns with SMNDC1: view

Primer Products

No data available for mRNA differential expression in normal tissues 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 35
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SMNDC1 34 35
  • 99.86 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SMNDC1 35
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMNDC1 34 35
  • 95.8 (n)
cow
(Bos Taurus)
Mammalia SMNDC1 34 35
  • 94.68 (n)
mouse
(Mus musculus)
Mammalia Smndc1 34 16 35
  • 90.06 (n)
rat
(Rattus norvegicus)
Mammalia Smndc1 34
  • 90.06 (n)
chicken
(Gallus gallus)
Aves SMNDC1 34 35
  • 85.29 (n)
lizard
(Anolis carolinensis)
Reptilia SMNDC1 35
  • 95 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smndc1 34
  • 76.05 (n)
African clawed frog
(Xenopus laevis)
Amphibia LOC397900 34
zebrafish
(Danio rerio)
Actinopterygii smndc1 34 35
  • 69.2 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7875 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006247 34
  • 52.6 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG17454 34 35
  • 51.08 (n)
worm
(Caenorhabditis elegans)
Secernentea smr-1 35
  • 31 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10154 35
  • 47 (a)
OneToOne
Species where no ortholog for SMNDC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for SMNDC1 Gene

Pseudogenes.org Pseudogenes for SMNDC1 Gene

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

No data available for Paralogs for SMNDC1 Gene

Variants for SMNDC1 Gene

Sequence variations from dbSNP and Humsavar for SMNDC1 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs1050754 -- 110,293,952(-) GTACC(A/C)CGGTT utr-variant-3-prime
rs1050755 -- 110,293,841(-) ATGGT(A/G)TGTAC utr-variant-3-prime
rs10509913 -- 110,294,021(+) TTCTA(C/T)TGAAG utr-variant-3-prime
rs10509914 -- 110,296,340(+) CCATA(C/T)TACCA intron-variant
rs10732802 -- 110,295,767(+) CTCCC(A/G)AGTAG intron-variant

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)

Relevant External Links for SMNDC1 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMNDC1 Gene

Disorders for SMNDC1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SMNDC1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
muscular atrophy
  • amyotrophia nos
spinal muscular atrophy
  • kugelberg-welander disease
proximal spinal muscular atrophy
  • spinal muscular atrophy
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SMNDC1

Genetic Association Database (GAD)
SMNDC1
Human Genome Epidemiology (HuGE) Navigator
SMNDC1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMNDC1
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. (Nat. Genet. 1998) 2 3 4 64
  2. Characterization of a gene encoding survival motor neuron (SMN)- related protein, a constituent of the spliceosome complex. (PMID: 9817934) Talbot K. … Davies K.E. (Hum. Mol. Genet. 1998) 2 3 4 64
  3. Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. (PMID: 22101937) Tripsianes K. … Sattler M. (Nat. Struct. Mol. Biol. 2011) 3 4 64
  4. Splicing factor SPF30 bridges an interaction between the prespliceosome protein U2AF35 and tri-small nuclear ribonucleoprotein protein hPrp3. (PMID: 18211889) Little J.T. … Jurica M.S. (J. Biol. Chem. 2008) 3 22 64
  5. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A. … Goate A. (Am. J. Hum. Genet. 2006) 3 46 64

Products for SMNDC1 Gene

Sources for SMNDC1 Gene

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