This gene encodes a small nuclear ribonucleoprotein that belongs to the SNRNP core protein family. The protein may act as a charged protein scaffold to promote SNRNP assembly or strengthen SNRNP-SNRNP interactions through nonspecific electrostatic contacts with RNA. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014] See more...

Aliases for SNRPD1 Gene

Aliases for SNRPD1 Gene

  • Small Nuclear Ribonucleoprotein D1 Polypeptide 2 3 5
  • Sm-D1 2 3 4
  • Small Nuclear Ribonucleoprotein Sm D1 3 4
  • SnRNP Core Protein D1 3 4
  • Sm-D Autoantigen 3 4
  • HsT2456 2 3
  • Small Nuclear Ribonucleoprotein D1 Polypeptide 16kDa Pseudogene 3
  • Small Nuclear Ribonucleoprotein D1 Polypeptide (16kD) 2
  • Small Nuclear Ribonucleoprotein D1 Polypeptide 16kDa 2
  • SNRPD1 5
  • SNRPD 3
  • SMD1 3

External Ids for SNRPD1 Gene

Previous HGNC Symbols for SNRPD1 Gene

  • SNRPD

Previous GeneCards Identifiers for SNRPD1 Gene

  • GC18P019067
  • GC18P018922
  • GC18P017444
  • GC18P017446
  • GC18P019192
  • GC18P016039

Summaries for SNRPD1 Gene

Entrez Gene Summary for SNRPD1 Gene

  • This gene encodes a small nuclear ribonucleoprotein that belongs to the SNRNP core protein family. The protein may act as a charged protein scaffold to promote SNRNP assembly or strengthen SNRNP-SNRNP interactions through nonspecific electrostatic contacts with RNA. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]

GeneCards Summary for SNRPD1 Gene

SNRPD1 (Small Nuclear Ribonucleoprotein D1 Polypeptide) is a Protein Coding gene. Diseases associated with SNRPD1 include Lupus Erythematosus and Neurotic Disorder. Among its related pathways are Transport of the SLBP independent Mature mRNA and mRNA Splicing - Minor Pathway. Gene Ontology (GO) annotations related to this gene include RNA binding. An important paralog of this gene is LSM4.

UniProtKB/Swiss-Prot Summary for SNRPD1 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:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Is also a component of the minor U12 spliceosome (PubMed:15146077). May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through non-specific electrostatic contacts with RNA (Probable).

Gene Wiki entry for SNRPD1 Gene

Additional gene information for SNRPD1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SNRPD1 Gene

Genomics for SNRPD1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SNRPD1 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 SNRPD1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SNRPD1

Top Transcription factor binding sites by QIAGEN in the SNRPD1 gene promoter:
  • AhR
  • Arnt
  • c-Ets-1
  • FOXO4
  • HEN1
  • HNF-1
  • HNF-1A
  • HSF1 (long)
  • HSF1short
  • Pax-4a

Genomic Locations for SNRPD1 Gene

Genomic Locations for SNRPD1 Gene
chr18:21,612,314-21,633,524
(GRCh38/hg38)
Size:
21,211 bases
Orientation:
Plus strand
chr18:19,192,228-19,210,417
(GRCh37/hg19)
Size:
18,190 bases
Orientation:
Plus strand

Genomic View for SNRPD1 Gene

Genes around SNRPD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNRPD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNRPD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNRPD1 Gene

Proteins for SNRPD1 Gene

  • Protein details for SNRPD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P62314-SMD1_HUMAN
    Recommended name:
    Small nuclear ribonucleoprotein Sm D1
    Protein Accession:
    P62314
    Secondary Accessions:
    • B5BTZ1
    • P13641

    Protein attributes for SNRPD1 Gene

    Size:
    119 amino acids
    Molecular mass:
    13282 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: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:21113136, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of the U1 snRNP (PubMed:19325628, PubMed:21113136, 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:21113136, 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 SNRPD1 Gene

neXtProt entry for SNRPD1 Gene

Post-translational modifications for SNRPD1 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 SNRPD1 Gene

No data available for DME Specific Peptides for SNRPD1 Gene

Domains & Families for SNRPD1 Gene

Gene Families for SNRPD1 Gene

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

Protein Domains for SNRPD1 Gene

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

Suggested Antigen Peptide Sequences for SNRPD1 Gene

GenScript: Design optimal peptide antigens:
  • Small nuclear ribonucleoprotein Sm D1 (Q7Z5A3_HUMAN)
  • snRNP core protein D1 (SMD1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P62314

UniProtKB/Swiss-Prot:

SMD1_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 SNRPD1: view

Function for SNRPD1 Gene

Molecular function for SNRPD1 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:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Is also a component of the minor U12 spliceosome (PubMed:15146077). May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through non-specific electrostatic contacts with RNA (Probable).

Phenotypes From GWAS Catalog for SNRPD1 Gene

Gene Ontology (GO) - Molecular Function for SNRPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding TAS,IBA 21873635
GO:0005515 protein binding IPI 9417867
GO:1990446 U1 snRNP binding IEA --
genes like me logo Genes that share ontologies with SNRPD1: view
genes like me logo Genes that share phenotypes with SNRPD1: view

Animal Model Products

CRISPR Products

miRNA for SNRPD1 Gene

miRTarBase miRNAs that target SNRPD1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SNRPD1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SNRPD1 Gene

Localization for SNRPD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SNRPD1 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 SNRPD1 gene
Compartment Confidence
nucleus 5
cytosol 5
mitochondrion 2
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for SNRPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000243 commitment complex IBA 21873635
GO:0005634 nucleus TAS,IMP 14524621
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005682 U5 snRNP IBA 21873635
genes like me logo Genes that share ontologies with SNRPD1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SNRPD1 Gene

Pathways & Interactions for SNRPD1 Gene

genes like me logo Genes that share pathways with SNRPD1: view

Pathways by source for SNRPD1 Gene

2 KEGG pathways for SNRPD1 Gene

Gene Ontology (GO) - Biological Process for SNRPD1 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:0006396 RNA processing IEA --
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with SNRPD1: view

No data available for SIGNOR curated interactions for SNRPD1 Gene

Drugs & Compounds for SNRPD1 Gene

(1) Drugs for SNRPD1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with SNRPD1: view

Transcripts for SNRPD1 Gene

mRNA/cDNA for SNRPD1 Gene

2 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
4 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 SNRPD1

Alternative Splicing Database (ASD) splice patterns (SP) for SNRPD1 Gene

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

Relevant External Links for SNRPD1 Gene

GeneLoc Exon Structure for
SNRPD1

Expression for SNRPD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SNRPD1 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SNRPD1 Gene



Protein tissue co-expression partners for SNRPD1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SNRPD1

SOURCE GeneReport for Unigene cluster for SNRPD1 Gene:

Hs.464734

Evidence on tissue expression from TISSUES for SNRPD1 Gene

  • Eye(4.1)
  • Nervous system(2.8)
  • Skin(2.6)
  • Muscle(2.5)
  • Heart(2.4)
  • Kidney(2.3)
  • Blood(2.3)
  • Liver(2.1)
  • Intestine(2)
genes like me logo Genes that share expression patterns with SNRPD1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SNRPD1 Gene

Orthologs for SNRPD1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SNRPD1 Gene

Organism Taxonomy Gene Similarity Type Details
Oppossum
(Monodelphis domestica)
Mammalia SNRPD1 31
  • 100 (a)
OneToOne
Chimpanzee
(Pan troglodytes)
Mammalia SNRPD1 30 31
  • 99.44 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia -- 31
  • 97 (a)
OneToMany
-- 31
  • 93 (a)
OneToMany
SNRPD1 30 31
  • 92.72 (n)
OneToMany
Mouse
(Mus musculus)
Mammalia Snrpd1 30 17 31
  • 94.4 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SNRPD1 30 31
  • 93.56 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Snrpd1 30
  • 93.28 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SNRPD1 31
  • 87 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SNRPD1 30 31
  • 81.85 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SNRPD1 31
  • 100 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia snrpd1 30
  • 79.83 (n)
Str.8924 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.8354 30
Zebrafish
(Danio rerio)
Actinopterygii snrpd1 30 31
  • 77.98 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta snRNP69D 32
  • 88 (a)
SmD1 30 31
  • 68.09 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007246 30
  • 70.92 (n)
Worm
(Caenorhabditis elegans)
Secernentea snr-3 30 31
  • 62.5 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SMD1 31 33
  • 38 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT4G02840 30
  • 67.38 (n)
Rice
(Oryza sativa)
Liliopsida Os04g0470200 30
  • 64.42 (n)
Os.12287 30
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.1761 31
  • 77 (a)
OneToOne
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes smd1 30
  • 66.67 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU00505 30
  • 61.54 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.15367 30
Species where no ortholog for SNRPD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • 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 SNRPD1 Gene

ENSEMBL:
Gene Tree for SNRPD1 (if available)
TreeFam:
Gene Tree for SNRPD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SNRPD1: view image

Paralogs for SNRPD1 Gene

Paralogs for SNRPD1 Gene

(5) SIMAP similar genes for SNRPD1 Gene using alignment to 4 proteins:

  • SMD1_HUMAN
  • J3QLI9_HUMAN
  • J3QLR7_HUMAN
  • Q7Z5A3_HUMAN

Pseudogenes.org Pseudogenes for SNRPD1 Gene

genes like me logo Genes that share paralogs with SNRPD1: view

Variants for SNRPD1 Gene

Additional dbSNP identifiers (rs#s) for SNRPD1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SNRPD1 Gene

Variant ID Type Subtype PubMed ID
esv29974 CNV loss 17803354

Variation tolerance for SNRPD1 Gene

Residual Variation Intolerance Score: 56.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.04; 0.95% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SNRPD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SNRPD1

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 SNRPD1 Gene

Disorders for SNRPD1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for SNRPD1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
lupus erythematosus
  • systemic lupus erythematosus
neurotic disorder
  • depressive neurosis
systemic lupus erythematosus
  • sle
basal ganglia cerebrovascular disease
autoimmune disease
  • autoimmune hypersensitivity disease
- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with SNRPD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SNRPD1 Gene

Publications for SNRPD1 Gene

  1. Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. (PMID: 28781166) Bertram K … Stark H (Cell 2017) 3 4
  2. Cryo-EM structure of a human spliceosome activated for step 2 of splicing. (PMID: 28076346) Bertram K … Lührmann R (Nature 2017) 3 4
  3. Molecular architecture of the human U4/U6.U5 tri-snRNP. (PMID: 26912367) Agafonov DE … Stark H (Science (New York, N.Y.) 2016) 3 4
  4. 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
  5. Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis. (PMID: 21516107) Leung AK … Li J (Nature 2011) 3 4

Products for SNRPD1 Gene

  • Signalway Proteins for SNRPD1

Sources for SNRPD1 Gene