Human Gene SNRPD2 (uc002pcw.3) Description and Page Index
  Description: Homo sapiens small nuclear ribonucleoprotein D2 polypeptide 16.5kDa (SNRPD2), transcript variant 1, mRNA.
RefSeq Summary (NM_004597): The protein encoded by this gene belongs to the small nuclear ribonucleoprotein core protein family. It is required for pre-mRNA splicing and small nuclear ribonucleoprotein biogenesis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009].
Transcript (Including UTRs)
   Position: hg19 chr19:46,190,712-46,195,443 Size: 4,732 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr19:46,190,811-46,195,146 Size: 4,336 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:46,190,712-46,195,443)mRNA (may differ from genome)Protein (118 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
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neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SMD2_HUMAN
DESCRIPTION: RecName: Full=Small nuclear ribonucleoprotein Sm D2; Short=Sm-D2; AltName: Full=snRNP core protein D2;
FUNCTION: Required for pre-mRNA splicing. Required for snRNP biogenesis (By similarity).
SUBUNIT: Identified in the spliceosome C complex. composed of AQR, ASCC3L1, C19orf29, CDC40, CDC5L. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome.
SUBCELLULAR LOCATION: Nucleus.
MISCELLANEOUS: In the autoimmune disease systemic lupus erythematosus, antinuclear antibodies are developed with Sm specificity.
SIMILARITY: Belongs to the snRNP core protein family.

-  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: 133.98 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2675.92 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 -97.63297-0.329 Picture PostScript Text
3' UTR -22.3099-0.225 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
IPR010920 - LSM_dom
IPR001163 - Ribonucl_LSM
IPR006649 - Ribonucl_LSM_euk/arc

Pfam Domains:
PF01423 - LSM domain

SCOP Domains:
50182 - Sm-like ribonucleoproteins

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1B34
- X-ray MuPIT

2Y9A
- X-ray

2Y9B
- X-ray
To conserve bandwidth, only the images from the first 3 structures are shown.
2Y9C - X-ray 2Y9D - X-ray 3CW1 - X-ray MuPIT
3PGW - X-ray 3S6N - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P62316
FrontTopSide
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

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

Biological Process:
GO:0000245 spliceosomal complex assembly
GO:0000387 spliceosomal snRNP assembly
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0051170 nuclear import

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005682 U5 snRNP
GO:0005685 U1 snRNP
GO:0005686 U2 snRNP
GO:0005687 U4 snRNP
GO:0005689 U12-type spliceosomal complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0030532 small nuclear ribonucleoprotein complex
GO:0034709 methylosome
GO:0034715 pICln-Sm protein complex
GO:0034719 SMN-Sm protein complex
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0070062 extracellular exosome
GO:0071007 U2-type catalytic step 2 spliceosome
GO:0071011 precatalytic spliceosome
GO:0071013 catalytic step 2 spliceosome


-  Descriptions from all associated GenBank mRNAs
  AK291912 - Homo sapiens cDNA FLJ76568 complete cds, highly similar to Homo sapiens small nuclear ribonucleoprotein D2 polypeptide 16.5kDa (SNRPD2), transcript variant 1, mRNA.
BC001930 - Homo sapiens small nuclear ribonucleoprotein D2 polypeptide 16.5kDa, mRNA (cDNA clone MGC:3995 IMAGE:2819767), complete cds.
BC000486 - Homo sapiens small nuclear ribonucleoprotein D2 polypeptide 16.5kDa, mRNA (cDNA clone MGC:8353 IMAGE:2819767), complete cds.
U15008 - Human SnRNP core protein Sm D2 mRNA, complete cds.
DQ891246 - Synthetic construct clone IMAGE:100003876; FLH176228.01X; RZPDo839A12122D small nuclear ribonucleoprotein D2 polypeptide 16.5kDa (SNRPD2) gene, encodes complete protein.
KJ892177 - Synthetic construct Homo sapiens clone ccsbBroadEn_01571 SNRPD2 gene, encodes complete protein.
DQ894432 - Synthetic construct Homo sapiens clone IMAGE:100008892; FLH176224.01L; RZPDo839A12121D small nuclear ribonucleoprotein D2 polypeptide 16.5kDa (SNRPD2) gene, encodes complete protein.
AB464218 - Synthetic construct DNA, clone: pF1KB6775, Homo sapiens SNRPD2 gene for small nuclear ribonucleoprotein D2 polypeptide, without stop codon, in Flexi system.
JD438018 - Sequence 419042 from Patent EP1572962.
JD185179 - Sequence 166203 from Patent EP1572962.
JD147545 - Sequence 128569 from Patent EP1572962.
JD418799 - Sequence 399823 from Patent EP1572962.
JD092953 - Sequence 73977 from Patent EP1572962.
JD433455 - Sequence 414479 from Patent EP1572962.
JD530783 - Sequence 511807 from Patent EP1572962.

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

BioCarta from NCI Cancer Genome Anatomy Project
h_smPathway - Spliceosomal Assembly

Reactome (by CSHL, EBI, and GO)

Protein P62316 (Reactome details) participates in the following event(s):

R-HSA-191790 Loading and methylation of Sm proteins onto SMN Complexes
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation
R-HSA-75080 Formation of AT-AC A complex
R-HSA-75079 Formation of AT-AC C complex
R-HSA-191830 snRNP nuclear import and release
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-191786 snRNP complex assembly
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-75081 Formation of AT-AC B Complex
R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-191763 snRNP:Snurportin complex formation
R-HSA-191784 snRNA Cap hypermethylation
R-HSA-191859 snRNP Assembly
R-HSA-194441 Metabolism of non-coding RNA
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-8953854 Metabolism of RNA
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA

-  Other Names for This Gene
  Alternate Gene Symbols: A8K797, NM_004597, NP_808210, P43330, P62316, SMD2_HUMAN, SNRPD1
UCSC ID: uc002pcw.3
RefSeq Accession: NM_004597
Protein: P62316 (aka SMD2_HUMAN)
CCDS: CCDS33053.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004597.5
exon count: 3CDS single in 3' UTR: no RNA size: 767
ORF size: 357CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 782.00frame shift in genome: no % Coverage: 98.17
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.