Human Gene SMNDC1 (uc001kzc.4)
  Description: Homo sapiens survival motor neuron domain containing 1 (SMNDC1), mRNA.
RefSeq Summary (NM_005871): 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].
Transcript (Including UTRs)
   Position: hg19 chr10:112,052,798-112,064,707 Size: 11,910 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr10:112,053,908-112,063,345 Size: 9,438 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:112,052,798-112,064,707)mRNA (may differ from genome)Protein (238 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPF30_HUMAN
DESCRIPTION: RecName: Full=Survival of motor neuron-related-splicing factor 30; AltName: Full=30 kDa splicing factor SMNrp; AltName: Full=SMN-related protein; AltName: Full=Survival motor neuron domain-containing protein 1;
FUNCTION: Necessary for spliceosome assembly. Overexpression causes apoptosis.
SUBUNIT: Associates with spliceosomes. Associates with U4/U5/U6 tri-snRNP and with U2 snRNP.
INTERACTION: Q14974:KPNB1; NbExp=2; IntAct=EBI-1052641, EBI-286758;
SUBCELLULAR LOCATION: Nucleus speckle. Nucleus, Cajal body. Note=Detected in nuclear speckles containing snRNP and in Cajal (coiled) bodies.
TISSUE SPECIFICITY: Detected at intermediate levels in skeletal muscle, and at low levels in heart and pancreas.
DOMAIN: The Tudor domain mediates association with dimethylarginines, which are common in snRNP proteins.
SIMILARITY: Belongs to the SMN family.
SIMILARITY: Contains 1 Tudor domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SMNDC1
CDC HuGE Published Literature: SMNDC1

-  MalaCards Disease Associations
  MalaCards Gene Search: SMNDC1
Diseases sorted by gene-association score: muscular atrophy (5), spinal muscular atrophy (4), proximal spinal muscular atrophy (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.20 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 316.33 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -46.20202-0.229 Picture PostScript Text
3' UTR -252.941110-0.228 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR010304 - Survival_motor_neuron
IPR002999 - Tudor

Pfam Domains:
PF06003 - Survival motor neuron protein (SMN)

SCOP Domains:
63748 - Tudor/PWWP/MBT

Protein Data Bank (PDB) 3-D Structure
MuPIT help
4A4F - NMR MuPIT 4A4H - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O75940
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000375 RNA splicing, via transesterification reactions
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0006915 apoptotic process
GO:0008380 RNA splicing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005737 cytoplasm
GO:0015030 Cajal body
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  BC039110 - Homo sapiens survival motor neuron domain containing 1, mRNA (cDNA clone IMAGE:4831086), with apparent retained intron.
BC011234 - Homo sapiens survival motor neuron domain containing 1, mRNA (cDNA clone MGC:17138 IMAGE:4153336), complete cds.
JD077949 - Sequence 58973 from Patent EP1572962.
JD248952 - Sequence 229976 from Patent EP1572962.
JD119931 - Sequence 100955 from Patent EP1572962.
JD295241 - Sequence 276265 from Patent EP1572962.
JD168662 - Sequence 149686 from Patent EP1572962.
JD326864 - Sequence 307888 from Patent EP1572962.
AF107463 - Homo sapiens splicing factor mRNA, complete cds.
JD094228 - Sequence 75252 from Patent EP1572962.
JD467990 - Sequence 449014 from Patent EP1572962.
JD289452 - Sequence 270476 from Patent EP1572962.
LF206916 - JP 2014500723-A/14419: Polycomb-Associated Non-Coding RNAs.
JD327932 - Sequence 308956 from Patent EP1572962.
AF083385 - Homo sapiens 30kDa splicing factor mRNA, complete cds.
AK314013 - Homo sapiens cDNA, FLJ94669, highly similar to Homo sapiens survival motor neuron domain containing 1 (SMNDC1), mRNA.
KJ892990 - Synthetic construct Homo sapiens clone ccsbBroadEn_02384 SMNDC1 gene, encodes complete protein.
LF359274 - JP 2014500723-A/166777: Polycomb-Associated Non-Coding RNAs.
LF359275 - JP 2014500723-A/166778: Polycomb-Associated Non-Coding RNAs.
JD272651 - Sequence 253675 from Patent EP1572962.
JD197126 - Sequence 178150 from Patent EP1572962.
JD297925 - Sequence 278949 from Patent EP1572962.
JD398144 - Sequence 379168 from Patent EP1572962.
MA442493 - JP 2018138019-A/14419: Polycomb-Associated Non-Coding RNAs.
MA594851 - JP 2018138019-A/166777: Polycomb-Associated Non-Coding RNAs.
MA594852 - JP 2018138019-A/166778: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein O75940 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B2RA27, D3DRB1, NM_005871, NP_005862, O75940, Q5T3K6, SMNR, SPF30, SPF30_HUMAN
UCSC ID: uc001kzc.4
RefSeq Accession: NM_005871
Protein: O75940 (aka SPF30_HUMAN or SF30_HUMAN)
CCDS: CCDS7565.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005871.3
exon count: 6CDS single in 3' UTR: no RNA size: 2043
ORF size: 717CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1634.00frame shift in genome: no % Coverage: 99.31
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.