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Aliases for SNRPD3 Gene

Aliases for SNRPD3 Gene

  • Small Nuclear Ribonucleoprotein D3 Polypeptide 2 3 5
  • Small Nuclear Ribonucleoprotein D3 Polypeptide 18kDa 2 3
  • SnRNP Core Protein D3 3 4
  • Sm-D3 3 4
  • Small Nuclear Ribonucleoprotein D3 Polypeptide (18kD) 2
  • Small Nuclear Ribonucleoprotein Sm D3 3
  • SMD3 3

External Ids for SNRPD3 Gene

Previous GeneCards Identifiers for SNRPD3 Gene

  • GC22P021648
  • GC22P023275
  • GC22P023276
  • GC22P024951
  • GC22P007901

Summaries for SNRPD3 Gene

Entrez Gene Summary for SNRPD3 Gene

  • This gene encodes a core component of the spliceosome, which is a nuclear ribonucleoprotein complex that functions in pre-mRNA splicing. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

GeneCards Summary for SNRPD3 Gene

SNRPD3 (Small Nuclear Ribonucleoprotein D3 Polypeptide) is a Protein Coding gene. Diseases associated with SNRPD3 include Lupus Erythematosus and Systemic Lupus Erythematosus. Among its related pathways are mRNA Splicing - Major Pathway and Processing of Capped Intronless Pre-mRNA. Gene Ontology (GO) annotations related to this gene include histone pre-mRNA DCP binding.

UniProtKB/Swiss-Prot for SNRPD3 Gene

  • Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. As part of the U7 snRNP it is involved in histone 3-end processing.

Gene Wiki entry for SNRPD3 Gene

Additional gene information for SNRPD3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SNRPD3 Gene

Genomics for SNRPD3 Gene

GeneHancer (GH) Regulatory Elements for SNRPD3 Gene

Promoters and enhancers for SNRPD3 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
GH22J024548 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 669.8 -2.0 -2041 8.9 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 SNRPD3 GGT1 GUCD1 ENSG00000272973 SGSM1 ENSG00000272578 UPB1 ADORA2A LOC100421614 ARL5AP4
GH22J024010 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 19.5 -543.8 -543818 2.6 PKNOX1 CLOCK FOXA2 ARID4B SIN3A ZNF2 YY1 ZNF766 E2F8 ZNF207 CABIN1 ENSG00000272973 ZDHHC8P1 MIF-AS1 SNRPD3 SUSD2 RN7SL268P GNAZ ZNF70 ENSG00000272578
GH22J024242 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE 19.3 -310.3 -310275 6.1 HDGF ARNT ZNF493 ZFP64 ARID4B SIN3A GLI4 ZBTB7B ZNF48 ZNF207 GGT5 ENSG00000272578 POM121L9P ZNF70 ENSG00000272973 SPECC1L SNRPD3 MIF-AS1 RN7SL268P SUSD2
GH22J024151 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 10.7 -399.7 -399650 8 HDGF FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZNF143 KLF13 SP3 CABIN1 SUSD2 MMP11 SPECC1L ZNF70 ENSG00000232545 SNRPD3 SMARCB1
GH22J023749 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.7 -803.5 -803507 4 HDGF ATF1 ZFP64 SIN3A ZNF2 ZBTB7B ZNF48 YY1 GTF3C2 POLR2B ZNF70 ENSG00000234353 MIF-AS1 SNRPD3 SMARCB1 CHCHD10 ENSG00000232545 VPREB3 ENSG00000272578
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SNRPD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SNRPD3 gene promoter:
  • CUTL1
  • YY1

Genomic Locations for SNRPD3 Gene

Genomic Locations for SNRPD3 Gene
chr22:24,555,503-24,609,980
(GRCh38/hg38)
Size:
54,478 bases
Orientation:
Plus strand
chr22:24,951,471-25,005,947
(GRCh37/hg19)
Size:
54,477 bases
Orientation:
Plus strand

Genomic View for SNRPD3 Gene

Genes around SNRPD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNRPD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNRPD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNRPD3 Gene

Proteins for SNRPD3 Gene

  • Protein details for SNRPD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P62318-SMD3_HUMAN
    Recommended name:
    Small nuclear ribonucleoprotein Sm D3
    Protein Accession:
    P62318
    Secondary Accessions:
    • B4DJP7
    • B5BU13
    • P43331

    Protein attributes for SNRPD3 Gene

    Size:
    126 amino acids
    Molecular mass:
    13916 Da
    Quaternary structure:
    • U1 snRNP is for instance composed of the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Component of the U7 snRNP complex, or U7 Sm protein core complex, at least composed of LSM10, LSM11, SNRPB, SNRPD3, SNRPE, SNRPF, SNRPG and U7 snRNA. Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG; catalyzes core snRNPs assembly. Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP.
    Miscellaneous:
    • In the autoimmune disease systemic lupus erythematosus, antinuclear antibodies are developed with Sm specificity.

    Three dimensional structures from OCA and Proteopedia for SNRPD3 Gene

    Alternative splice isoforms for SNRPD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SNRPD3 Gene

Post-translational modifications for SNRPD3 Gene

  • Methylated on arginine residues by PRMT5 and PRMT7; probable asymmetric dimethylation which is required for assembly and biogenesis of snRNPs.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SNRPD3 Gene

No data available for DME Specific Peptides for SNRPD3 Gene

Domains & Families for SNRPD3 Gene

Gene Families for SNRPD3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SNRPD3 Gene

Suggested Antigen Peptide Sequences for SNRPD3 Gene

Graphical View of Domain Structure for InterPro Entry

P62318

UniProtKB/Swiss-Prot:

SMD3_HUMAN :
  • Belongs to the snRNP core protein family.
Family:
  • Belongs to the snRNP core protein family.
genes like me logo Genes that share domains with SNRPD3: view

Function for SNRPD3 Gene

Molecular function for SNRPD3 Gene

UniProtKB/Swiss-Prot Function:
Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. As part of the U7 snRNP it is involved in histone 3-end processing.

Phenotypes From GWAS Catalog for SNRPD3 Gene

Gene Ontology (GO) - Molecular Function for SNRPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IPI 18082603
GO:0005515 protein binding IPI 11714716
GO:0019899 enzyme binding IPI 17709427
GO:0030620 U2 snRNA binding IPI 18082603
GO:0070034 telomerase RNA binding IPI 18082603
genes like me logo Genes that share ontologies with SNRPD3: view
genes like me logo Genes that share phenotypes with SNRPD3: view

miRNA for SNRPD3 Gene

miRTarBase miRNAs that target SNRPD3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SNRPD3 Gene

Localization for SNRPD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SNRPD3 Gene

Cytoplasm, cytosol. Nucleus. Note=SMN-mediated assembly into core snRNPs occurs in the cytosol before SMN-mediated transport to the nucleus to be included in spliceosomes.

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 SNRPD3 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for SNRPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000243 commitment complex IBA --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex TAS,IEA 7527560
GO:0005682 U5 snRNP IBA --
genes like me logo Genes that share ontologies with SNRPD3: view

Pathways & Interactions for SNRPD3 Gene

genes like me logo Genes that share pathways with SNRPD3: view

Pathways by source for SNRPD3 Gene

Gene Ontology (GO) - Biological Process for SNRPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000245 spliceosomal complex assembly IBA --
GO:0000387 spliceosomal snRNP assembly TAS,IEA --
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006396 RNA processing IEA --
genes like me logo Genes that share ontologies with SNRPD3: view

No data available for SIGNOR curated interactions for SNRPD3 Gene

Drugs & Compounds for SNRPD3 Gene

No Compound Related Data Available

Transcripts for SNRPD3 Gene

mRNA/cDNA for SNRPD3 Gene

Unigene Clusters for SNRPD3 Gene

Small nuclear ribonucleoprotein D3 polypeptide 18kDa:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SNRPD3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4
SP1:
SP2: -
SP3: -

Relevant External Links for SNRPD3 Gene

GeneLoc Exon Structure for
SNRPD3
ECgene alternative splicing isoforms for
SNRPD3

Expression for SNRPD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SNRPD3 Gene

Protein differential expression in normal tissues from HIPED for SNRPD3 Gene

This gene is overexpressed in Nasal epithelium (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SNRPD3 Gene



Protein tissue co-expression partners for SNRPD3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SNRPD3 Gene:

SNRPD3

SOURCE GeneReport for Unigene cluster for SNRPD3 Gene:

Hs.356549

Evidence on tissue expression from TISSUES for SNRPD3 Gene

  • Nervous system(4.6)
  • Lung(4.3)
genes like me logo Genes that share expression patterns with SNRPD3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SNRPD3 Gene

Orthologs for SNRPD3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SNRPD3 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia -- 34
  • 100 (a)
OneToMany
-- 34
  • 99 (a)
OneToMany
SNRPD3 33
  • 91.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SNRPD3 34
  • 100 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SNRPD3 34
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SNRPD3 34 33
  • 99.74 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Snrpd3 33
  • 92.59 (n)
mouse
(Mus musculus)
Mammalia Snrpd3 16 34 33
  • 91.8 (n)
cow
(Bos Taurus)
Mammalia SNRPD3 34 33
  • 87.2 (n)
OneToOne
chicken
(Gallus gallus)
Aves SNRPD3 34 33
  • 85.71 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SNRPD3 34
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia snrpd3 33
  • 84.13 (n)
Str.17086 33
zebrafish
(Danio rerio)
Actinopterygii snrpd3l 34
  • 96 (a)
OneToMany
snrpd3 34 33
  • 76.72 (n)
OneToMany
wufa18f04 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8795 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012380 33
  • 72.96 (n)
fruit fly
(Drosophila melanogaster)
Insecta SmD3 34 35 33
  • 70.72 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea snr-1 34 33
  • 64.13 (n)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGL157C 33
  • 62.6 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SMD3 36 34
  • 46 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G20580 33
  • 60.07 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.5543 33
soybean
(Glycine max)
eudicotyledons Gma.5905 33
rice
(Oryza sativa)
Liliopsida Os03g0240800 33
  • 63.27 (n)
barley
(Hordeum vulgare)
Liliopsida Hv.2388 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6100 34
  • 71 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes smd3 33
  • 64.96 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU03625 33
  • 59.88 (n)
Species where no ortholog for SNRPD3 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SNRPD3 Gene

ENSEMBL:
Gene Tree for SNRPD3 (if available)
TreeFam:
Gene Tree for SNRPD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SNRPD3: view image

Paralogs for SNRPD3 Gene

(2) SIMAP similar genes for SNRPD3 Gene using alignment to 3 proteins:

  • SMD3_HUMAN
  • B4DJP7_HUMAN
  • H3BT13_HUMAN
genes like me logo Genes that share paralogs with SNRPD3: view

No data available for Paralogs for SNRPD3 Gene

Variants for SNRPD3 Gene

Sequence variations from dbSNP and Humsavar for SNRPD3 Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1000070163 -- 24,555,808(+) G/C 5_prime_UTR_variant, non_coding_transcript_variant
rs1000147489 -- 24,564,784(+) CCC/CCCC intron_variant
rs1000351879 -- 24,554,766(+) C/T upstream_transcript_variant
rs1000384492 -- 24,555,086(+) T/C upstream_transcript_variant
rs1000490117 -- 24,558,930(+) C/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SNRPD3 Gene

Variant ID Type Subtype PubMed ID
nsv9884 CNV gain+loss 18304495
nsv7350 OTHER inversion 18451855
nsv588744 CNV gain 21841781
nsv526567 CNV gain 19592680
nsv1110863 OTHER inversion 24896259
nsv1109459 CNV deletion 24896259
nsv1057819 CNV gain 25217958
nsv1055830 CNV gain 25217958
esv3893463 CNV gain 25118596
esv3575443 CNV gain 25503493
esv3568312 CNV loss 25503493
esv2724068 CNV deletion 23290073
esv2724041 CNV deletion 23290073
dgv8039n54 CNV gain 21841781
dgv4528n100 CNV gain 25217958

Variation tolerance for SNRPD3 Gene

Residual Variation Intolerance Score: 49% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SNRPD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SNRPD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SNRPD3 Gene

Disorders for SNRPD3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SNRPD3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
lupus erythematosus
  • systemic lupus erythematosus
systemic lupus erythematosus
  • sle
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SNRPD3

genes like me logo Genes that share disorders with SNRPD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SNRPD3 Gene

Publications for SNRPD3 Gene

  1. cDNA cloning of the Sm proteins D2 and D3 from human small nuclear ribonucleoproteins: evidence for a direct D1-D2 interaction. (PMID: 7527560) Lehmeier T … Lührmann R (Proceedings of the National Academy of Sciences of the United States of America 1994) 2 3 4 58
  2. Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis. (PMID: 21516107) Leung AK … Li J (Nature 2011) 3 4 58
  3. Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution. (PMID: 19325628) Pomeranz Krummel DA … Nagai K (Nature 2009) 3 4 58
  4. An assembly chaperone collaborates with the SMN complex to generate spliceosomal SnRNPs. (PMID: 18984161) Chari A … Fischer U (Cell 2008) 3 4 58
  5. Two distinct arginine methyltransferases are required for biogenesis of Sm-class ribonucleoproteins. (PMID: 17709427) Gonsalvez GB … Matera AG (The Journal of cell biology 2007) 3 4 58

Products for SNRPD3 Gene

Sources for SNRPD3 Gene

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