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Aliases for SNRPD2 Gene

Aliases for SNRPD2 Gene

  • Small Nuclear Ribonucleoprotein D2 Polypeptide 2 3 5
  • SnRNP Core Protein D2 2 3 4
  • Small Nuclear Ribonucleoprotein D2 Polypeptide 16.5kDa 2 3
  • SNRPD1 3 4
  • Sm-D2 3 4
  • Small Nuclear Ribonucleoprotein D2 Polypeptide (16.5kD) 2
  • Small Nuclear Ribonucleoprotein Sm D2 3
  • 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. Among its related pathways are Transport of the SLBP independent Mature mRNA and mRNA Splicing - Major Pathway. GO annotations related to this gene include poly(A) RNA binding.

UniProtKB/Swiss-Prot for SNRPD2 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.

Gene Wiki entry for SNRPD2 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SNRPD2 Gene

Genomics for SNRPD2 Gene

Regulatory Elements for SNRPD2 Gene

Enhancers for SNRPD2 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
GH19F045667 0.4 ENCODE 26 +24.0 24001 2.4 HDGF PKNOX1 ARNT WRNIP1 SIN3A YBX1 ZNF2 FOS KLF13 SP3 SNRPD2 ENSG00000267395 ENSG00000259605 ENSG00000268810 SIX5 RELB DMWD GIPR GC19P045675
GH19F045680 1 Ensembl ENCODE 19.8 +8.9 8920 5.5 HDGF ATF1 ZFP64 ARID4B SIN3A ZNF48 ZNF2 ZNF207 ZNF143 ZNF548 SNRPD2 CCDC61 IGFL4 ENSG00000268810 GIPR GC19M045670 QPCTL
GH19F045422 1.1 ENCODE 19 +268.1 268108 3.3 MLX CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZNF610 ZNF180 ENSG00000267395 CCDC61 ENSG00000259605 ENSG00000268810 FBXO46 ENSG00000269148 ENSG00000266958 SNRPD2 ERCC1
GH19F045690 0.6 ENCODE 18.9 +0.1 97 3.2 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 ENSG00000267395 DMWD ENSG00000268810 SNRPD2 CCDC61 QPCTL SIX5 FBXO46 BHMG1 EML2
GH19F046600 0.2 ENCODE 18.9 -909.8 -909826 4.6 CREB3L1 ZFP64 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 ZNF610 ZC3H4 ENSG00000267395 ENSG00000259605 CCDC61 CCDC9 FBXO46 ENSG00000269148 ENSG00000268810 SLC1A5 SNRPD2
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SNRPD2 on UCSC Golden Path with GeneCards custom track

Promoters for SNRPD2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000217042 269 2601 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1

Genomic Location for SNRPD2 Gene

Chromosome:
19
Start:
45,687,454 bp from pter
End:
45,692,569 bp from pter
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:
    • 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. 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 Lys 98
  • Modification sites at PhosphoSitePlus

Other Protein References for SNRPD2 Gene

No data available for DME Specific Peptides for SNRPD2 Gene

Domains & Families for SNRPD2 Gene

Protein Domains for SNRPD2 Gene

Suggested Antigen Peptide Sequences for SNRPD2 Gene

GenScript: Design optimal peptide antigens:

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

No data available for Gene Families for SNRPD2 Gene

Function for SNRPD2 Gene

Molecular function for SNRPD2 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.

Gene Ontology (GO) - Molecular Function for SNRPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 9417867
GO:0044822 poly(A) RNA binding IDA 22658674
GO:1990446 U1 snRNP binding IEA --
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

miRNA for SNRPD2 Gene

Inhibitory RNA Products

Flow Cytometry Products

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.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SNRPD2 Gene COMPARTMENTS Subcellular localization image for SNRPD2 gene
Compartment Confidence
cytosol 5
extracellular 5
nucleus 5

Gene Ontology (GO) - Cellular Components for SNRPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex TAS 1701240
GO:0005682 U5 snRNP IBA --
GO:0005685 U1 snRNP 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 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

Transcripts for SNRPD2 Gene

Unigene Clusters for SNRPD2 Gene

Small nuclear ribonucleoprotein D2 polypeptide 16.5kDa:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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
ECgene alternative splicing isoforms 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, PaxDb, MaxQB, and MOPED for SNRPD2 Gene



Protein tissue co-expression partners for SNRPD2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SNRPD2 Gene:

SNRPD2

SOURCE GeneReport for Unigene cluster for SNRPD2 Gene:

Hs.515472
genes like me logo Genes that share expression patterns with SNRPD2: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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 34 35
  • 99.15 (n)
oppossum
(Monodelphis domestica)
Mammalia SNRPD2 35
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Gm5449 35
  • 95 (a)
OneToOne
Snrpd2 34 16
  • 91.24 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SNRPD2 35
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SNRPD2 34 35
  • 93.22 (n)
dog
(Canis familiaris)
Mammalia SNRPD2 34 35
  • 93.22 (n)
rat
(Rattus norvegicus)
Mammalia Snrpd2 34
  • 91.81 (n)
lizard
(Anolis carolinensis)
Reptilia SNRPD2 35
  • 99 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia snrpd2 34
  • 80.23 (n)
Str.10758 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.4271 34
zebrafish
(Danio rerio)
Actinopterygii snrpd2 34 35
  • 84.18 (n)
Dr.12513 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.778 34
fruit fly
(Drosophila melanogaster)
Insecta CG1249 36
  • 88 (a)
SmD2 34 35
  • 79.71 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003936 34
  • 74.78 (n)
worm
(Caenorhabditis elegans)
Secernentea snr-4 34 35
  • 71.05 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D09284g 34
  • 58.42 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR277W 34
  • 56.19 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SMD2 34 35 37
  • 55.35 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G62840 34
  • 74.44 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3324 34
rice
(Oryza sativa)
Liliopsida Os05g0314100 34
  • 75.56 (n)
Os.24812 34
barley
(Hordeum vulgare)
Liliopsida Hv.2981 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 75 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU03778 34
  • 63.24 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes smd2 34
  • 57.27 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4211 34
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)

Paralogs for SNRPD2 Gene

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

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

Sequence variations from dbSNP and Humsavar for SNRPD2 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs10403723 -- 45,688,570(+) TCCTG(C/T)ATGGA intron-variant
rs10413179 -- 45,690,299(+) tgcac(G/T)ccagc intron-variant
rs10426987 -- 45,692,152(+) AAGGC(A/G)GTCTG intron-variant, upstream-variant-2KB
rs10611704 -- 45,690,497(+) CAAAA(-/CAAAA)GAAAA intron-variant, upstream-variant-2KB
rs111254684 -- 45,693,242(+) GATGG(C/T)CTTGG intron-variant, upstream-variant-2KB

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)

Relevant External Links for SNRPD2 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SNRPD2 Gene

Disorders for SNRPD2 Gene

Relevant External Links for SNRPD2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SNRPD2

No disorders were found for SNRPD2 Gene.

No data available for MalaCards , 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. … Luehrmann R. (Proc. Natl. Acad. Sci. U.S.A. 1994) 2 3 4 64
  2. Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis. (PMID: 21516107) Leung A.K. … Li J. (Nature 2011) 3 4 64
  3. An assembly chaperone collaborates with the SMN complex to generate spliceosomal SnRNPs. (PMID: 18984161) Chari A. … Fischer U. (Cell 2008) 3 4 64
  4. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J. … Lucas S.M. (Nature 2004) 3 4 64
  5. The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. (PMID: 15146077) Will C.L. … Luehrmann R. (RNA 2004) 3 4 64

Products for SNRPD2 Gene

Sources for SNRPD2 Gene

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