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SNRPA Gene(Protein Coding)

Small Nuclear Ribonucleoprotein Polypeptide A

GCID:
GC19P040750
GIFtS:
56
Genes Participants
UDN Logo

Aliases for SNRPA Gene

Aliases for SNRPA Gene

  • Small Nuclear Ribonucleoprotein Polypeptide A 2 3 5
  • U1 SnRNP A 3 4
  • U1-A 3 4
  • U1A 3 4
  • U1 Small Nuclear Ribonucleoprotein A 3
  • U1 Small Nuclear RNP-Specific A 3
  • U1 SnRNP-Specific Protein A 3
  • Mud1 3

External Ids for SNRPA Gene

Previous GeneCards Identifiers for SNRPA Gene

  • GC19P041896
  • GC19P041648
  • GC19P045932
  • GC19P045948
  • GC19P041256
  • GC19P037690

Summaries for SNRPA Gene

Entrez Gene Summary for SNRPA Gene

  • The protein encoded by this gene associates with stem loop II of the U1 small nuclear ribonucleoprotein, which binds the 5' splice site of precursor mRNAs and is required for splicing. The encoded protein autoregulates itself by polyadenylation inhibition of its own pre-mRNA via dimerization and has been implicated in the coupling of splicing and polyadenylation. [provided by RefSeq, Oct 2010]

GeneCards Summary for SNRPA Gene

SNRPA (Small Nuclear Ribonucleoprotein Polypeptide A) is a Protein Coding gene. Diseases associated with SNRPA include Connective Tissue Disease and Suppression Amblyopia. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. GO annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is SNRPB2.

UniProtKB/Swiss-Prot for SNRPA Gene

  • Component of the spliceosomal U1 snRNP, which is essential for recognition of the pre-mRNA 5 splice-site and the subsequent assembly of the spliceosome. U1 snRNP is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. SNRPA binds stem loop II of U1 snRNA. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. May bind preferentially to the 5-UGCAC-3 motif on RNAs.

Gene Wiki entry for SNRPA Gene

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

Genomics for SNRPA Gene

Products:

  1. Regulatory Element

Regulatory Elements for SNRPA Gene

Enhancers for SNRPA 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
GH19G040713 2.1 FANTOM5 Ensembl ENCODE dbSUPER 80.6 -32.3 -32290 9.2 CREB3L1 DMAP1 FEZF1 YY1 ZNF143 ZNF416 ZNF548 SP3 NFYC SSRP1 SNRPA FBL ITPKC ENSG00000205041 ENSG00000269843 CCDC97 PSMC4 NUMBL COQ8B ENSG00000269069
GH19G040796 2.1 FANTOM5 Ensembl ENCODE dbSUPER 49.3 +51.7 51701 11.8 CREB3L1 MLX AGO1 ZFP64 DMAP1 YBX1 FEZF1 YY1 ZNF416 ZNF143 ENSG00000205041 SNRPA ENSG00000269843 ENSG00000269069 NUMBL ITPKC FBL COQ8B CCDC97 EGLN2
GH19G041294 2.1 FANTOM5 Ensembl ENCODE dbSUPER 49.1 +552.7 552660 16.8 MLX CREB3L1 AGO1 ZFP64 FEZF1 DMAP1 YBX1 YY1 ZNF416 ZNF143 SNRPA ZNF526 ENSG00000269843 ZNF574 TGFB1 TMEM91 ITPKC HNRNPUL1 CCDC97 B9D2
GH19G040830 1.6 Ensembl ENCODE dbSUPER 60.3 +82.2 82150 4.6 PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SNRPA ENSG00000269843 FBL ITPKC CCDC97 ENSG00000205041 PSMC4 COQ8B ENSG00000269069 RNU6-195P
GH19G040747 1.8 FANTOM5 ENCODE dbSUPER 48.2 +2.1 2125 9.8 MLX CREB3L1 ZFP64 DMAP1 YBX1 FEZF1 YY1 ZNF416 ZNF143 ZNF263 ENSG00000269843 SNRPA ENSG00000205041 FBL COQ8B ITPKC CCDC97 NUMBL C19orf54 SERTAD3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SNRPA on UCSC Golden Path with GeneCards custom track

Promoters for SNRPA Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000109586 663 2601 MLX CREB3L1 ZFP64 FEZF1 DMAP1 YBX1 YY1 ZNF416 ZNF143 SP3

Transcription factor binding sites by QIAGEN in the SNRPA gene promoter:

Genomic Location for SNRPA Gene

Chromosome:
19
Start:
40,750,637 bp from pter
End:
40,765,392 bp from pter
Size:
14,756 bases
Orientation:
Plus strand

Genomic View for SNRPA Gene

Genes around SNRPA on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SNRPA Gene

Proteins for SNRPA Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    P09012-SNRPA_HUMAN
    Recommended name:
    U1 small nuclear ribonucleoprotein A
    Protein Accession:
    P09012

    Protein attributes for SNRPA Gene

    Size:
    282 amino acids
    Molecular mass:
    31280 Da
    Quaternary structure:
    • U1 snRNP is 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. Interacts with SFPQ; component of a snRNP-free complex with SFPQ.

    Three dimensional structures from OCA and Proteopedia for SNRPA Gene

neXtProt entry for SNRPA Gene

Protein Expression for SNRPA Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SNRPA Gene

  • Ubiquitination at isoforms=20, Lys60, isoforms=88, Lys96, isoforms=98, isoforms=268, and isoforms=276
  • Modification sites at PhosphoSitePlus

Other Protein References for SNRPA Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SNRPA Gene

Domains & Families for SNRPA Gene

Gene Families for SNRPA Gene

HGNC:

Protein Domains for SNRPA Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for SNRPA Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P09012

UniProtKB/Swiss-Prot:

SNRPA_HUMAN :
  • Belongs to the RRM U1 A/B family.
Family:
  • Belongs to the RRM U1 A/B family.
genes like me logo Genes that share domains with SNRPA: view

Function for SNRPA Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for SNRPA Gene

GENATLAS Biochemistry:
samll ribonucleoprotein U1,A polypeptide
UniProtKB/Swiss-Prot Function:
Component of the spliceosomal U1 snRNP, which is essential for recognition of the pre-mRNA 5 splice-site and the subsequent assembly of the spliceosome. U1 snRNP is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. SNRPA binds stem loop II of U1 snRNA. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. May bind preferentially to the 5-UGCAC-3 motif on RNAs.

Gene Ontology (GO) - Molecular Function for SNRPA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,IDA 19561594
GO:0005515 protein binding IPI 9848648
GO:0030619 U1 snRNA binding IBA --
GO:0035614 snRNA stem-loop binding IBA --
genes like me logo Genes that share ontologies with SNRPA: view
genes like me logo Genes that share phenotypes with SNRPA: view

Animal Model Products

miRNA for SNRPA Gene

miRTarBase miRNAs that target SNRPA

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 SNRPA Gene

Localization for SNRPA Gene

Subcellular locations from UniProtKB/Swiss-Prot for SNRPA Gene

Nucleus.

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 SNRPA gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
mitochondrion 2
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for SNRPA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS,IDA --
GO:0005681 spliceosomal complex IDA 9731529
GO:0005685 U1 snRNP IDA 21113136
GO:0030529 intracellular ribonucleoprotein complex IEA --
genes like me logo Genes that share ontologies with SNRPA: view

Pathways & Interactions for SNRPA Gene

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

Pathways by source for SNRPA Gene

1 BioSystems pathway for SNRPA Gene
1 KEGG pathway for SNRPA Gene

Gene Ontology (GO) - Biological Process for SNRPA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
GO:1900363 regulation of mRNA polyadenylation IEA --
genes like me logo Genes that share ontologies with SNRPA: view

No data available for SIGNOR curated interactions for SNRPA Gene

Drugs & Compounds for SNRPA Gene

Products:

  1. Drug

(5) Drugs for SNRPA Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Malonic acid Experimental Pharma Target 0

(3) Additional Compounds for SNRPA Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SNRPA: view

Transcripts for SNRPA Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for SNRPA Gene

(1) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(488) Selected AceView cDNA sequences:
(11) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SNRPA Gene

Small nuclear ribonucleoprotein polypeptide A:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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

ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b · 3c · 3d ^ 4a · 4b · 4c · 4d ^ 5 ^ 6a · 6b · 6c · 6d ^ 7a · 7b · 7c ^ 8 ^ 9
SP1: - - - -
SP2: - - - - - - - - - - -
SP3: - - - - - -
SP4: - - - - - -
SP5: - - - - - -
SP6: - - - -
SP7: - - -
SP8: -
SP9: - -
SP10: -

Relevant External Links for SNRPA Gene

GeneLoc Exon Structure for
SNRPA
ECgene alternative splicing isoforms for
SNRPA

Expression for SNRPA Gene

Products:

  1. Primer

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

mRNA expression in normal human tissues for SNRPA Gene
mRNA expression by BioGPS for SNRPA GenemRNA expression by GTEx for SNRPA Gene

Protein differential expression in normal tissues from HIPED for SNRPA Gene

This gene is overexpressed in Lymph node (6.6).

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



Protein tissue co-expression partners for SNRPA Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SNRPA Gene:

SNRPA

SOURCE GeneReport for Unigene cluster for SNRPA Gene:

Hs.466775

Evidence on tissue expression from TISSUES for SNRPA Gene

  • Liver(4.5)
  • Lung(4.5)
  • Nervous system(4)
  • Muscle(2.7)
  • Heart(2.4)
  • Intestine(2.3)
  • Blood(2.2)
  • Kidney(2.2)
  • Eye(2.1)
  • Skin(2.1)
  • Spleen(2.1)
genes like me logo Genes that share expression patterns with SNRPA: view

Primer Products

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 SNRPA Gene

Orthologs for SNRPA Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SNRPA Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia SNRPA 34 35
  • 99.65 (n)
oppossum
(Monodelphis domestica)
 Mammalia SNRPA 35
  • 94 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Snrpa 35
  • 94 (a)
 OneToMany
Gm5145 35
  • 90 (a)
 OneToMany
dog
(Canis familiaris)
 Mammalia SNRPA 34 35
  • 91.61 (n)
cow
(Bos Taurus)
 Mammalia SNRPA 34 35
  • 91.13 (n)
rat
(Rattus norvegicus)
 Mammalia Snrpa 34
  • 89.44 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia SNRPA 35
  • 75 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia SNRPA 35
  • 90 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia snrpa 34
  • 73.78 (n)
Str.3059 34
African clawed frog
(Xenopus laevis)
 Amphibia snf-prov 34
zebrafish
(Danio rerio)
 Actinopterygii snrpa 34 35
  • 76.22 (n)
-- 34
fruit fly
(Drosophila melanogaster)
 Insecta snf 34 35
  • 75.08 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP011637 34
  • 70.51 (n)
worm
(Caenorhabditis elegans)
 Secernentea rnp-2 34 35
  • 60.03 (n)
rnp-3 35
  • 50 (a)
 ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes MSL1 35 37
  • 27 (a)
 OneToMany
thale cress
(Arabidopsis thaliana)
 eudicotyledons U1A 34
  • 54.99 (n)
Alicante grape
(Vitis vinifera)
 eudicotyledons Vvi.7167 34
rice
(Oryza sativa)
 Liliopsida Os05g0154800 34
  • 60.78 (n)
Os.9766 34
barley
(Hordeum vulgare)
 Liliopsida Hv.1400 34
wheat
(Triticum aestivum)
 Liliopsida Ta.5442 34
corn
(Zea mays)
 Liliopsida Zm.3121 34
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.10455 35
  • 55 (a)
 OneToMany
bread mold
(Neurospora crassa)
 Ascomycetes NCU08034 34
  • 48.24 (n)
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes usp102 34
  • 45.68 (n)
Species where no ortholog for SNRPA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • 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)
  • 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)

Evolution for SNRPA Gene

ENSEMBL:
Gene Tree for SNRPA (if available)
TreeFam:
Gene Tree for SNRPA (if available)

Paralogs for SNRPA Gene

Paralogs for SNRPA Gene

(2) SIMAP similar genes for SNRPA Gene using alignment to 7 proteins:

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

Variants for SNRPA Gene

Sequence variations from dbSNP and Humsavar for SNRPA Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs1000077433 -- 40,754,194(+) CGCCT(C/G)CCGAA intron-variant
rs1000302033 -- 40,760,104(+) TCACT(A/C/G)CAACC intron-variant
rs1000377746 -- 40,749,653(+) AACAG(C/G)GGTCT intron-variant, nc-transcript-variant, upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs1000434082 -- 40,765,592(+) AAATG(A/G)AATCC downstream-variant-500B
rs1000571615 -- 40,764,434(+) ATGCC(A/G)ATGGA intron-variant

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

Variant ID Type Subtype PubMed ID
esv21537 CNV loss 19812545
nsv1160619 CNV deletion 26073780
nsv833832 CNV loss 17160897

Variation tolerance for SNRPA Gene

Residual Variation Intolerance Score: 10.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.47; 10.19% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SNRPA Gene

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

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

Disorders for SNRPA Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
connective tissue disease
  • connective tissue disorder
suppression amblyopia
  • strabismic amblyopia
- elite association - COSMIC cancer census association via MalaCards
Search SNRPA in MalaCards View complete list of genes associated with diseases

Relevant External Links for SNRPA

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SNRPA
genes like me logo Genes that share disorders with SNRPA: view

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

Publications for SNRPA Gene

  1. The snRNP-free U1A (SF-A) complex(es): identification of the largest subunit as PSF, the polypyrimidine-tract binding protein-associated splicing factor. (PMID: 9848648) Lutz C.S. … Alwine J.C. (RNA 1998) 3 4 22 64
  2. Tertiary structure of RBD2 and backbone dynamics of RBD1 and RBD2 of the human U1A protein determined by NMR spectroscopy. (PMID: 9265619) Lu J. … Hall K.B. (Biochemistry 1997) 3 4 22 64
  3. Structural basis of the RNA-binding specificity of human U1A protein. (PMID: 9312034) Allain F.H.-T. … Varani G. (EMBO J. 1997) 3 4 22 64
  4. Solution structure of the N-terminal RNP domain of U1A protein: the role of C-terminal residues in structure stability and RNA binding. (PMID: 8609632) Avis J.M. … Neuhaus D. (J. Mol. Biol. 1996) 3 4 22 64
  5. Crystal structure at 1.92-A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. (PMID: 7984237) Oubridge C. … Nagai K. (Nature 1994) 3 4 22 64

Products for SNRPA Gene

  • Addgene plasmids for SNRPA

Sources for SNRPA Gene

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