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] See more...

Aliases for SNRPD2 Gene

Aliases for SNRPD2 Gene

  • Small Nuclear Ribonucleoprotein D2 Polypeptide 2 3 5
  • SnRNP Core Protein D2 2 3 4
  • Sm-D2 2 3 4
  • Small Nuclear Ribonucleoprotein D2 Polypeptide 16.5kDa 2 3
  • Small Nuclear Ribonucleoprotein Sm D2 3 4
  • SNRPD1 3 4
  • Small Nuclear Ribonucleoprotein D2 Polypeptide (16.5kD) 2
  • SNRPD2 5
  • SMD2 3

External Ids for SNRPD2 Gene

Previous HGNC Symbols for SNRPD2 Gene

  • SNRPD1

Previous GeneCards Identifiers for SNRPD2 Gene

  • GC19M046834
  • GC19M046581
  • GC19M050866
  • GC19M050882
  • GC19M046190
  • GC19M042619

Summaries for SNRPD2 Gene

Entrez Gene Summary for SNRPD2 Gene

  • 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]

GeneCards Summary for SNRPD2 Gene

SNRPD2 (Small Nuclear Ribonucleoprotein D2 Polypeptide) is a Protein Coding gene. Diseases associated with SNRPD2 include Basal Ganglia Cerebrovascular Disease and Spinal Muscular Atrophy. Among its related pathways are Transport of the SLBP independent Mature mRNA and mRNA Splicing - Minor Pathway.

UniProtKB/Swiss-Prot Summary for SNRPD2 Gene

  • Plays role in pre-mRNA splicing as core component of the SMN-Sm complex that mediates spliceosomal snRNP assembly and as component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:18984161, PubMed:19325628, PubMed:23333303, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes (PubMed:11991638, PubMed:28502770, PubMed:28781166, PubMed:28076346). Is also a component of the minor U12 spliceosome (PubMed:15146077).

Gene Wiki entry for SNRPD2 Gene

Additional gene information for SNRPD2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SNRPD2 Gene

Genomics for SNRPD2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SNRPD2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SNRPD2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SNRPD2

Top Transcription factor binding sites by QIAGEN in the SNRPD2 gene promoter:
  • AML1a
  • AP-2gamma
  • AREB6
  • CP2
  • CUTL1
  • GATA-1
  • p300
  • PPAR-gamma1
  • PPAR-gamma2
  • SREBP-1a

Genomic Locations for SNRPD2 Gene

Genomic Locations for SNRPD2 Gene
chr19:45,687,454-45,692,569
(GRCh38/hg38)
Size:
5,116 bases
Orientation:
Minus strand
chr19:46,190,712-46,195,827
(GRCh37/hg19)
Size:
5,116 bases
Orientation:
Minus strand

Genomic View for SNRPD2 Gene

Genes around SNRPD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNRPD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNRPD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNRPD2 Gene

Proteins for SNRPD2 Gene

  • Protein details for SNRPD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P62316-SMD2_HUMAN
    Recommended name:
    Small nuclear ribonucleoprotein Sm D2
    Protein Accession:
    P62316
    Secondary Accessions:
    • A8K797
    • J3KPM5
    • P43330

    Protein attributes for SNRPD2 Gene

    Size:
    118 amino acids
    Molecular mass:
    13527 Da
    Quaternary structure:
    • Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:19325628, PubMed:21516107, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). 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 (PubMed:10025403, PubMed:19325628, PubMed:21516107, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of the U1 snRNP (PubMed:19325628, PubMed:25555158). The U1 snRNP is composed of the U1 snRNA and the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C (PubMed:19325628, PubMed:25555158). Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 (PubMed:26912367). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (PubMed:15146077). 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 SNRPD2 Gene

    Alternative splice isoforms for SNRPD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SNRPD2 Gene

Post-translational modifications for SNRPD2 Gene

  • Ubiquitination at Lys98
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SNRPD2 Gene

Domains & Families for SNRPD2 Gene

Gene Families for SNRPD2 Gene

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

Protein Domains for SNRPD2 Gene

InterPro:
Blocks:
  • Like-Sm ribonucleoprotein-related, core
ProtoNet:

Suggested Antigen Peptide Sequences for SNRPD2 Gene

GenScript: Design optimal peptide antigens:
  • snRNP core protein D2 (SMD2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P62316

UniProtKB/Swiss-Prot:

SMD2_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 SNRPD2: view

Function for SNRPD2 Gene

Molecular function for SNRPD2 Gene

UniProtKB/Swiss-Prot Function:
Plays role in pre-mRNA splicing as core component of the SMN-Sm complex that mediates spliceosomal snRNP assembly and as component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:18984161, PubMed:19325628, PubMed:23333303, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes (PubMed:11991638, PubMed:28502770, PubMed:28781166, PubMed:28076346). Is also a component of the minor U12 spliceosome (PubMed:15146077).

Phenotypes From GWAS Catalog for SNRPD2 Gene

Gene Ontology (GO) - Molecular Function for SNRPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 9417867
genes like me logo Genes that share ontologies with SNRPD2: view
genes like me logo Genes that share phenotypes with SNRPD2: view

Animal Model Products

CRISPR Products

miRNA for SNRPD2 Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SNRPD2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SNRPD2 Gene

Localization for SNRPD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SNRPD2 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. {ECO:0000305}.

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 SNRPD2 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SNRPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 28076346
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex TAS 1701240
GO:0005682 U5 snRNP IBA 21873635
GO:0005685 U1 snRNP IBA,IDA 21113136
genes like me logo Genes that share ontologies with SNRPD2: view

Pathways & Interactions for SNRPD2 Gene

genes like me logo Genes that share pathways with SNRPD2: view

Pathways by source for SNRPD2 Gene

1 KEGG pathway for SNRPD2 Gene

Gene Ontology (GO) - Biological Process for SNRPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000245 spliceosomal complex assembly TAS 7527560
GO:0000387 spliceosomal snRNP assembly IBA,TAS --
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA,TAS 1701240
genes like me logo Genes that share ontologies with SNRPD2: view

No data available for SIGNOR curated interactions for SNRPD2 Gene

Drugs & Compounds for SNRPD2 Gene

(1) Drugs for SNRPD2 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Dihydroartemisinin Experimental, Investigational Pharma Target, ligand 115
genes like me logo Genes that share compounds with SNRPD2: view

Transcripts for SNRPD2 Gene

mRNA/cDNA for SNRPD2 Gene

4 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
8 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 SNRPD2

Alternative Splicing Database (ASD) splice patterns (SP) for SNRPD2 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c · 7d · 7e
SP1: - - - -
SP2: - - -
SP3: - - -
SP4: - - -
SP5: - - - - -
SP6: - -

Relevant External Links for SNRPD2 Gene

GeneLoc Exon Structure for
SNRPD2

Expression for SNRPD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SNRPD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SNRPD2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (9.2) and Tlymphocyte (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SNRPD2 Gene



Protein tissue co-expression partners for SNRPD2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SNRPD2

SOURCE GeneReport for Unigene cluster for SNRPD2 Gene:

Hs.515472

Evidence on tissue expression from TISSUES for SNRPD2 Gene

  • Lung(4.8)
  • Blood(4.6)
  • Nervous system(4.2)
  • Skin(4)
  • Liver(3.1)
  • Muscle(3)
  • Heart(2.7)
  • Kidney(2.7)
  • Intestine(2.6)
  • Bone marrow(2.5)
  • Lymph node(2.5)
  • Spleen(2.5)
  • Thyroid gland(2.4)
  • Stomach(2.4)
  • Eye(2.2)
genes like me logo Genes that share expression patterns with SNRPD2: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SNRPD2 Gene

Orthologs for SNRPD2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SNRPD2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SNRPD2 30 31
  • 99.15 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SNRPD2 31
  • 99 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SNRPD2 31
  • 95 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Gm5449 31
  • 95 (a)
OneToOne
Snrpd2 30 17
  • 91.24 (n)
Dog
(Canis familiaris)
Mammalia SNRPD2 30 31
  • 93.22 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SNRPD2 30 31
  • 93.22 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Snrpd2 30
  • 91.81 (n)
Lizard
(Anolis carolinensis)
Reptilia SNRPD2 31
  • 99 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia snrpd2 30
  • 80.23 (n)
Str.10758 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.4271 30
Zebrafish
(Danio rerio)
Actinopterygii snrpd2 30 31
  • 84.18 (n)
OneToOne
Dr.12513 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.778 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG1249 32
  • 88 (a)
SmD2 30 31
  • 79.71 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003936 30
  • 74.78 (n)
Worm
(Caenorhabditis elegans)
Secernentea snr-4 30 31
  • 71.05 (n)
OneToOne
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D09284g 30
  • 58.42 (n)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AGR277W 30
  • 56.19 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SMD2 30 31 33
  • 55.35 (n)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT3G62840 30
  • 74.44 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3324 30
Rice
(Oryza sativa)
Liliopsida Os05g0314100 30
  • 75.56 (n)
Os.24812 30
Barley
(Hordeum vulgare)
Liliopsida Hv.2981 30
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 75 (a)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU03778 30
  • 63.24 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes smd2 30
  • 57.27 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.4211 30
Species where no ortholog for SNRPD2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chicken (Gallus gallus)
  • 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)
  • 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)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SNRPD2 Gene

ENSEMBL:
Gene Tree for SNRPD2 (if available)
TreeFam:
Gene Tree for SNRPD2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SNRPD2: view image

Paralogs for SNRPD2 Gene

(2) SIMAP similar genes for SNRPD2 Gene using alignment to 3 proteins:

  • SMD2_HUMAN
  • K7EJB5_HUMAN
  • K7ERG4_HUMAN

Pseudogenes.org Pseudogenes for SNRPD2 Gene

genes like me logo Genes that share paralogs with SNRPD2: view

No data available for Paralogs for SNRPD2 Gene

Variants for SNRPD2 Gene

Additional dbSNP identifiers (rs#s) for SNRPD2 Gene

Structural Variations from Database of Genomic Variants (DGV) for SNRPD2 Gene

Variant ID Type Subtype PubMed ID
esv3644509 CNV gain 21293372
nsv960855 CNV duplication 23825009

Variation tolerance for SNRPD2 Gene

Residual Variation Intolerance Score: 43.1% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SNRPD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SNRPD2

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 SNRPD2 Gene

Disorders for SNRPD2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SNRPD2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
basal ganglia cerebrovascular disease
spinal muscular atrophy
  • progressive muscular atrophy
- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with SNRPD2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SNRPD2 Gene

Publications for SNRPD2 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
  2. Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. (PMID: 28781166) Bertram K … Stark H (Cell 2017) 3 4
  3. Cryo-EM structure of a human spliceosome activated for step 2 of splicing. (PMID: 28076346) Bertram K … Lührmann R (Nature 2017) 3 4
  4. Molecular architecture of the human U4/U6.U5 tri-snRNP. (PMID: 26912367) Agafonov DE … Stark H (Science (New York, N.Y.) 2016) 3 4
  5. Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition. (PMID: 25555158) Kondo Y … Nagai K (eLife 2015) 3 4

Products for SNRPD2 Gene

  • Signalway Proteins for SNRPD2

Sources for SNRPD2 Gene